Intramolecular Component Research Articles

Coupled Rotary Motion in Molecular Motors.

Biological molecular machines play a pivotal role in sustaining life by producing a controlled and directional motion. Artificial molecular machines aim to mimic this motion, to exploit and tune the nanoscale produced motion to power dynamic molecular systems. The precise control, transfer, and amplification of the molecular-level motion is crucial to harness the potential of synthetic molecular motors. It is intriguing to establish how directional motor rotation can be utilized to drive secondary motions in other subunits of a multicomponent molecular machine. The challenge to design sophisticated synthetic machines involving multiple motorized elements presents fascinating opportunities for achieving unprecedented functions, but these remain almost unexplored due to their extremely intricate behavior. Here we show intrinsic coupled rotary motion in light-driven overcrowded-alkene based molecular motors. Thus far, molecular motors with two rotors have been understood to undergo independent rotation of each subunit. The new bridged-isoindigo motor design revealed an additional dimension to the motor's unidirectional operation mechanism where communication between the rotors occurs. An unprecedented double metastable state intermediate bridges the rotation cycles of the two rotor subunits. Our findings demonstrate how neighboring motorized subunits can affect each other and thereby drastically change the motor's functioning. Controlling the embedded entanglement of active intramolecular components sets the stage for more advanced artificial molecular machines.

Polaron absorption in aligned conjugated polymer films: breakdown of adiabatic treatments and going beyond the conventional mid-gap state model.

This study provides the first experimental polarized intermolecular and intramolecular optical absorption components of field-induced polarons in regioregular poly(3-hexylthiophene-2,5-diyl), rr-P3HT, a polymer semiconductor. Highly aligned rr-P3HT thin films were prepared by a high temperature shear-alignment process that orients polymer backbones along the shearing direction. rr-P3HT in-plane molecular orientation was measured by electron diffraction, and out-of-plane orientation was measured through series of synchrotron X-ray scattering techniques. Then, with molecular orientation quantified, polarized charge modulation spectroscopy was used to probe mid-IR polaron absorption in the ℏω = 0.075 - 0.75 eV range and unambiguously assign intermolecular and intramolecular optical absorption components of hole polarons in rr-P3HT. This data represents the first experimental quantification of these polarized components and allowed long-standing theoretical predictions to be compared to experimental results. The experimental data is discrepant with predictions of polaron absorption based on an adiabatic framework that works under the Born-Oppenheimer approximation, but the data is entirely consistent with a more recent nonadiabatic treatment of absorption based on a modified Holstein Hamiltonian. This nonadiabatic treatment was used to show that both intermolecular and intramolecular polaron coherence break down at length scales significantly smaller than estimated structural coherence in either direction. This strongly suggests that polaron delocalization is fundamentally limited by energetic disorder in rr-P3HT.

Rational control of π-conjugation and CT component in hybridized local and charge transfer molecules for high performance deep blue emitters

The ratio of locally excited (LE) and charge transfer (CT) components plays a key role in harvesting the “hot” triplet excitons through high-lying reverse intersystem crossing (hRISC) in organic light-emitting materials. Herein, two blue carbazole derivative isomers 2,7-Cz(DOFCP)2 and 3,6-Cz(DOFCP)2 were designed with A-π-D-π-A structures. The localized π-conjugation and intramolecular charge transfer components ratio was rationally varied by the substitute position of 9,9-dioctylfluorenyl (DOF) π-bridge on the carbazolyl donor unit. Both of the emitters exhibited hybridized local and charge transfer (HLCT) characteristics, and 2,7-Cz(DOFCP)2 with prolonged localized π-conjugation nature realized a smaller energy splitting (ΔES2-T3) and higher fluorescence quantum yield. The OLEDs based on the emitters achieved deep blue and nearly standard blue electroluminescence with the CIE coordinates of (0.153, 0.063) and (0.153, 0.091), and maximum EQEs of 5.57% and 7.37% that was beyond the conventional fluorescence devices, respectively. This work would provide insights for promoting the luminescence performance of the HLCT molecules by adjusting the LE/CT proportion in the excited states.

Cooperativity in Shape-Persistent Bis-(Zn-salphen) Catalysts for Efficient Cyclic Carbonate Synthesis under Mild Conditions.

A series of conformationally rigid (Zn-salphen)2 complexes with a planar bridging component (xanthene or dibenzofuran) are described. Conformational changes for these assemblies are essentially limited to the axial rotation of the Zn-salphen moieties; however, such geometric constraints crucially permit the subtle tuning of the intermetallic separation and geometry to potentially enhance catalytic activity (and cooperative effects). The complexes have been investigated as catalysts in conjunction with nBu4NI for the coupling of CO2 with epoxides. Selected dibenzofuran derivatives are significantly more active for the production of cyclic carbonate than their mononuclear analogues under identical conditions and concentrations of Zn sites. High initial turnover frequencies (up to 29 000 h-1; 14 500 h-1 per Zn, using 10 bar of CO2 at 95 °C) and excellent efficiencies under mild conditions (1 bar of CO2 at 55 °C) have been achieved. Kinetic studies using in situ (ReactIR) spectroscopy and density functional theory calculations have been performed, which reveal the existence of an intramolecular rate component and a preference for the cooperative pathway as well as transition states that depict the Zn sites operating in tandem. Taken together, these results provide strong evidence of cooperative reactivity in these Zn2 catalysts.

Spotlight on Charge-Transfer Excitons in Crystalline Textured n-Alkyl Anilino Squaraine Thin Films

Prototypical n-alkyl terminated anilino squaraines for photovoltaic applications show characteristic double-hump absorption features peaking in the green and deep-red spectral range. These signatures result from coupling of an intramolecular Frenkel exciton and an intermolecular charge transfer exciton. Crystalline, textured thin films suitable for polarized spectro-microscopy have been obtained for compounds with n-hexyl (nHSQ) and n-octyl (nOSQ) terminal alkyl chains. The here released triclinic crystal structure of nOSQ is similar to the known nHSQ crystal structure. Consequently, crystallites from both compounds show equal pronounced linear dichroism with two distinct polarization directions. The difference in polarization angle between the two absorbance maxima cannot be derived by spatial considerations from the crystal structure alone but requires theoretical modeling. Using an essential state model, the observed polarization behavior was discovered to depend on the relative contributions of the intramolecular Frenkel exciton and the intermolecular charge transfer exciton to the total transition dipole moment. For both nHSQ and nOSQ, the contribution of the charge transfer exciton to the total transition dipole moment was found to be small compared to the intramolecular Frenkel exciton. Therefore, the net transition dipole moment is largely determined by the intramolecular component resulting in a relatively small mutual difference between the polarization angles. Ultimately, the molecular alignment within the micro-textured crystallites can be deduced and, with that, the excited state transitions can be spotted.

N-(4-Eth-oxy-2,5-di-nitro-phen-yl)acetamide.

In the title compound, C10H11N3O6, the torsion angles about the bonds to the benzene ring are less than 4°, except for the nitro groups, which are twisted out of the ring plane by 25.27 (3) and 43.63 (2)°. The N-H group forms a bifurcated hydrogen bond, with an intra-molecular component to a nitro group O atom and an inter-molecular component to the other nitro group, thereby forming chains propagating in the [010] direction. Several weak C-H⋯O inter-actions are also present.

Concomitant Polymorphism in an Organic Solid: Molecular and Crystal Structure and Intra- and Intermolecular Potential Contributions to tert-Butyl and Methyl Group Rotation.

We investigate the relationship between structure (crystal and molecular) and tert-butyl and methyl group dynamics in 2-(tert-butyl)-9-(4-(tert-butyl)phenyl)anthracene. Powder and single-crystal X-ray diffraction, taken together, show that different polycrystalline samples recrystallized from different solvents have different amounts of at least four polymorphs (crystallites having different crystal structures), of which we have identified three by single crystal X-ray diffraction. The molecules in the asymmetric units of the different crystal structures differ by the dihedral angle the tert-butylphenyl group makes with the anthracene moiety. Ab initio electronic structure calculations on the isolated molecule show that very little intramolecular energy is required to change this angle over a range of about 60° which is probably the origin of the concomitant polymorphism (crystals of more than one polymorph in a polycrystalline sample). Solid state 1 H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments support the powder and single-crystal X-ray results and provide average NMR activation energies (closely related to rotational barriers) for the rotation of the tert-butyl groups and their constituent methyl groups. These barriers have both an intramolecular and an intermolecular component. The latter is sensitive to the crystal structure. The intramolecular components of the rotational barriers of the two tert-butyl groups in the isolated molecule are investigated with ab initio electronic structure calculations.

How do phonons relax molecular spins?

The coupling between electronic spins and lattice vibrations is fundamental for driving relaxation in magnetic materials. The debate over the nature of spin-phonon coupling dates back to the 1940s, but the role of spin-spin, spin-orbit, and hyperfine interactions has never been fully established. Here, we present a comprehensive study of the spin dynamics of a crystal of Vanadyl-based molecular qubits by means of first-order perturbation theory and first-principles calculations. We quantitatively determine the role of the Zeeman, hyperfine, and electronic spin dipolar interactions in the direct mechanism of spin relaxation. We show that, in a high magnetic field regime, the modulation of the Zeeman Hamiltonian by the intramolecular components of the acoustic phonons dominates the relaxation mechanism. In low fields, hyperfine coupling takes over, with the role of spin-spin dipolar interaction remaining the less important for the spin relaxation.

Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation.

Crystal simulations provide useful tools, along with solution simulations, to test nucleic acid force fields, but should be interpreted with care owing to the difficulty of establishing the environmental conditions needed to reproduce experimental crystal packing. These challenges underscore the need to construct proper protocols for carrying out crystal simulations and analyzing results to identify the origin of deviations from crystallographic data. Toward this end, we introduce a novel framework for B-factor decomposition into additive intramolecular, rotational, and translational atomic fluctuation components and partitioning of each of these components into individual asymmetric unit and lattice contributions. We apply the framework to a benchmark set of A-DNA, Z-DNA, and B-DNA double helix systems of various chain lengths. Overall, the intramolecular deviations from the crystal were quite small (≤1.0 Å), suggesting high accuracy of the force field, whereas crystal packing was not well reproduced. The present work establishes a framework to conduct and analyze crystal simulations that ultimately take on issues of crystal packing and can provide insight into nucleic acid force fields.

Construction of Equations of the State to Describe Isothermal Compression of Some Molecular Crystals of Nitro-Compounds

We propose an approach to construct the equations of state of molecular crystals of nitro compounds. The approach allows to describe isothermal compression, and is based on the division of the Helmholtz free energy into thermal and "cold" parts. It turns out that the "cold" part can be divided into the intramolecular and intermolecular components, while the low-frequency and high-frequency vibrations can be distinguished in the thermal part. We propose to approximate the low-frequency component of the thermal part of the internal energy and the pressure of a molecular crystal by the Debye approximation. In order to describe the intermolecular energy of the Van der Waals interaction, we propose a potential that closes on the heat of sublimation of a molecular crystal. The "cold" part of pressure is determined by the change in intramolecular energy. We assume the "cold" part of pressure to be constant, and use the condition that the pressure is equal to 1 atm. under normal conditions in order to determine this part. This division of the Helmholtz energy allows to obtain explicitly the expressions for all thermodynamic values in the equations of state. In this paper, we assume the linear dependence of the Gruneisen coefficient on the volume. The use of a more complex relationship is not necessary, since we consider the isothermal compression, and the thermal component makes an insignificant contribution to the total pressure. We use the obtained dependences of thermodynamic values on temperature and volume in order to find the coefficients related to the known experimental data. A comparative analysis of the calculated and experimental values of the specific volumes of the molecular crystal of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) as a function of pressure shows their coincidence with an accuracy of 1%.

Intramolecular and intermolecular bifurcated hydrogen bonds in 2‐pyrrolyl‐7‐hydroxy‐2‐methylidene‐2,3‐dihydro‐1H‐inden‐1‐one

AbstractCyclic and linear dimers as well as the solvate H‐bonded complexes of the Z and E isomers of 2‐pyrrolyl‐7‐hydroxy‐2‐methylidene‐2,3‐dihydro‐1H‐inden‐1‐one 1 were investigated by theoretical calculations, and their formation was proved by FT‐IR and UV spectroscopy. In dimers, both strengthening and weakening of the intramolecular component of the bifurcated hydrogen bond are observed depending on the type of the formed intermolecular hydrogen bond. The effect of proton donors MeOH, HCN, and proton acceptor DMSO on the intramolecular components in solvent H‐bonded complexes is discussed. A larger energy gap in the 1‐E than in 1‐Z isomer allows to predict photoinduced isomeric transition 1‐Е → 1‐Z in nonpolar aprotic solvents.

Simulations of the OKE Response in Simple Liquids Using a Polarizable and a Nonpolarizable Force Field.

Recently polarizable force fields are becoming increasingly popular for molecular dynamics simulations. As the signal obtained in the optical Kerr effect (OKE) experiment is due to the polarizability dynamics of the investigated system, a study is conducted in order to compare the experimental results with those obtained with the polarizable AMOEBA force field. The comparison is made in the frequency domain; however, time domain data are also included. The selected molecular systems are the isotropic carbon tetrachloride molecule, the anisotropic chloroform, carbon disulfide and acetone molecules, and the hydrogen-bonded water and methanol molecules. Different dipole-induced-dipole (DID) method variants are used for calculation of the OKE response, showing the importance of use of the all-atom approach with preoptimized atomic polarizabilities. In order to obtain a good intermolecular to intramolecular components amplitude ratio, the isotropic polarizability in the Thole correction needs to be updated between iterations. The convergence of the spectra calculated with different DID variants is also considered, and the approach that appears to be the best gives a very good approximation after three iterations. The comparison of the experimental and simulated spectra shows a rather good agreement for the non-hydrogen-bonded molecules, although the contribution of the reorientation of anisotropic molecules is overestimated. In the case of the hydrogen-bonded molecules, the theoretical spectra are far from the experimental ones. The highly overestimated librational bands indicate excessive polarizability anisotropy introduced by the potential model. Finally, in order to verify the significance of different components of the AMOEBA model, it is gradually simplified and compared with a simple reference potential model. Removal of polarizability shows a tremendous change in the case of hydrogen-bonded liquids, whereas for the other molecules it is of minor importance. The non-hydrogen-bonded liquids are, however, more sensitive to the presence of atomic multipoles in the model.

ОПРЕДЕЛЕНИЕ ВЫРАЖЕНИЯ ИЗОБАРИЧЕСКОГО КОЭФФИЦИЕНТА ОБЪЕМНОГО РАСШИРЕНИЯ ДЛЯ НЕКОТОРЫХ МОЛЕКУЛЯРНЫХ КРИСТАЛЛОВ НИТРОСОЕДИНЕНИЙ

A type of equations on the state of molecular crystals of nitro compounds is suggested based on dividing Helmholtz free energy into intramolecular and intermolecular components. It is suggested to approach the thermal part of the internal energy and pressure of a molecular crystal with Debye approximation for intermolecular component, and with Einstein approximation for intramolecular component. This division of Helmholtz energy allowed to obtain clear expressions for all thermodynamic quantities being part of the equations of state. The suggestion that isothermal sound speed of a molecular crystal at the temperature of 0 K is determined solely by elastic characteristics of the crystal made it possible to obtain the dependency of Gruneisen coefficient on volume. The dependencies of thermodynamic quantities on temperature and volume determined in this work were used to build an analog of Gruneisen equation for molecular crystals, and to determine the dependency of isobaric coefficient of crystal volume expansion on temperature. It turned out that to obtain calculated values of volumes of unit cells of triamyno trinitrobenzene (TATB) crystals while integrating Gruneisen equation as per temperature, a high-temperature approximation may be used for Debye specific thermal capacity function. The obtained theoretical dependency of isobaric coefficient of crystal volume expansion on temperature indicates at the automatic meeting the condition of its tending to zero while the temperature tends to zero. The comparative analysis of the calculated and experimental values of volumes of unit cells of molecular crystals of 1,3,5 – 2,4,6 – trinitrobenzene (TATB) depending on the temperature showed that they concur satisfactorily to the accuracy of no more than 3 %

Functional versatile bipolar 3,3′-dimethyl-9,9′-bianthracene derivatives as an efficient host and deep-blue emitter

A new family of bipolar fluorinated 3,3′-dimethyl-9,9′-bianthracene derivatives (MBAnFs) have been synthesized, characterized and applied as deep-blue emitters and host materials in fluorescent organic light-emitting devices (OLEDs). Fine tuning the emission characteristics could be achieved by varying the position and the number of the F substituents on the two phenyl rings attached to MBAn core. Remarkably, 10,10′-bis(4-fluorophenyl)-3,3′-dimethyl-9,9′-bianthracene (MBAn-(4)-F)-based OLEDs showed an excellent performance. Both non-doped and doped multilayer OLEDs based on MBAn-(4)-F achieved the maximum external quantum efficiency (EQEmax) of 6.11% and 6.65% with Commission Internationale de L'Eclairage (CIE) coordinates of (0.155, 0.058) and (0.153, 0.055), respectively, matching the requirement of European Broadcasting Union standard of CIE (0.15, 0.06) very well. Furthermore, when doping blue-emitting p-bis(p-N,N-diphenyl-aminostyryl)-benzene (DSA-ph) into MBAn-(4)-F as a light-emitting layer (EML), the device achieved an astonishing current efficiency of 23.01 cd A−1 and a record-setting EQE of 11.52% with negligible efficiency roll-off, compared with other DSA-ph-based OLEDs. These results are attributed to the well-controlled bipolar characteristic of the MABn-(4)-F, leading to a better charge balance in the EML. In addition, the combination of the locally emissive component and twisted intramolecular charge-transfer component in one excited state can significantly enhance the singlet generation fraction in OLEDs.

The contribution of various network knots during the deformation of ethylene copolymers and nanocomposites based on them

An analysis of the deformation mechanism and changes in mechanical parameters of low-crystallinity ethylene–octene copolymers of various densities and modified with detonation nanodiamonds is performed through the use of models based on the statistical theory of rubber-like elasticity. Experimental data were processed in terms of the Haward model with allowance for the non-Gaussian statistics of macromolecules at high strain and limited extensibility and the so-called “slip-link” model, which considers the density of labile knots and permanent entanglements. Despite obvious simplifications, both models attribute the discovered extrema of the concentration dependences of mechanical properties at low concentrations of nanodiamonds to the change in the number of segments between network knots and the following change in elastic modulus (Haward model) or to the number of labile and permanent knots (“slip-link” model), a circumstance that verifies the nucleating effect of nanodiamonds. It was found that the relative increase in density of each type of knot significantly depends on the degree of crystallinity of the matrix and the concentration of the modifier. Deformation calorimetry showed that tensile and cyclic loading of the investigated systems are followed by changes in internal energy. The roles of its intramolecular and intermolecular components at the various stages of deformation and the causes of their changes were estimated. The correlation between energy effects and the transformation of the structuring and parameters of the used models was determined.

(1)H and (19)F spin-lattice relaxation and CH3 or CF3 reorientation in molecular solids containing both H and F atoms.

The dynamics of methyl (CH3) and fluoromethyl (CF3) groups in organic molecular (van der Waals) solids can be exploited to survey their local environments. We report solid state (1)H and (19)F spin-lattice relaxationexperiments in polycrystalline 3-trifluoromethoxycinnamic acid, along with an X-ray diffraction determination of the molecular and crystal structure, to investigate the intramolecular and intermolecular interactions that determine the properties that characterize the CF3 reorientation. The molecule is of no particular interest; it simply provides a motionless backbone (on the nuclear magnetic resonance(NMR) time scale) to investigate CF3 reorientation occurring on the NMR time scale. The effects of (19)F-(19)F and (19)F-(1)H spin-spin dipolar interactions on the complicated nonexponential NMRrelaxation provide independent inputs into determining a model for CF3 reorientation. As such, these experiments provide much more information than when only one spin species (usually (1)H) is present. In Sec. IV, which can be read immediately after the Introduction without reading the rest of the paper, we compare the barrier to CH3 and CF3 reorientation in seven organic solids and separate this barrier into intramolecular and intermolecular components.

Energy transfer dynamics and kinetics of elementary processes (promoted) by gas-phase CO2 -N2 collisions: Selectivity control by the anisotropy of the interaction.

In this work, we exploit a new formulation of the potential energy and of the related computational procedures, which embodies the coupling between the intra and intermolecular components, to characterize possible propensities of the collision dynamics in energy transfer processes of interest for simulation and control of phenomena occurring in a variety of equilibrium and nonequilibrium environments. The investigation reported in the paper focuses on the prototype CO2 -N2 system, whose intramolecular component of the interaction is modeled in terms of a many body expansion while the intermolecular component is modeled in terms of a recently developed bonds-as-interacting-molecular-centers' approach. The main advantage of this formulation of the potential energy surface is that of being (a) truly full dimensional (i.e., all the variations of the coordinates associated with the molecular vibrations and rotations on the geometrical and electronic structure of the monomers, are explicitly taken into account without freezing any bonds or angles), (b) more flexible than other usual formulations of the interaction and (c) well suited for fitting procedures better adhering to accurate ab initio data and sensitive to experimental arrangement dependent information. Specific attention has been given to the fact that a variation of vibrational and rotational energy has a higher (both qualitative and quantitative) impact on the energy transfer when a more accurate formulation of the intermolecular interaction (with respect to that obtained when using rigid monomers) is adopted. This makes the potential energy surface better suited for the kinetic modeling of gaseous mixtures in plasma, combustion and atmospheric chemistry computational applications. © 2016 Wiley Periodicals, Inc.

Developing accurate molecular mechanics force fields for conjugated molecular systems.

A rapid method to parameterize the intramolecular component of classical force fields for complex conjugated molecules is proposed. The method is based on a procedure of force matching with a reference electronic structure calculation. It is particularly suitable for those applications where molecular dynamics simulations are used to generate structures that are therefore analysed by electronic structure methods, because it is possible to build force fields that are consistent with electronic structure calculations that follow classical simulations. Such applications are commonly encountered in organic electronics, spectroscopy of complex systems and photobiology (e.g. photosynthetic systems). We illustrate the method by parameterizing the force fields of a molecule used in molecular semiconductors (2,2-dicyanovinyl-capped S,N-heteropentacene or DCV-SN5), a polymeric semiconductor (thieno[3,2-b]thiophene-diketopyrrolopyrrole TT-DPP) and a chromophore embedded in a protein environment (15,16-dihydrobiliverdin or DBV) where several hundreds of parameters need to be optimized in parallel.

The bellamy relationship and the nature of the H-bond. 2-Haloethanols

IR-spectroscopy data show that the intramolecular H-bond in alcohols with the general formula XCH2CH2OH (X = F, Cl, Br) in a solution is mainly of a nonspecific nature. Molecules of 2-haloethanol form three-center complexes with an external H-bond acceptor. The intramolecular component of their bifurcated bond causes a stronger spectroscopic effect as compared to the two-center H-bond of ethanol or 1-propanol.

What we can learn from the norms of one-particle density matrices, and what we can't: some results for interstate properties in model singlet fission systems.

The utility of the norms of one-particle density matrices, ∥γ∥, for understanding the trends in electronic properties is discussed. Using several model systems that are relevant in the context of singlet fission (butadiene, octatetraene, and ethylene dimer), the dependence of interstate properties (such as transition dipole moments and nonadiabatic couplings, NACs) on molecular geometries is investigated. ∥γ∥ contains the principal information about the changes in electronic states involved, such as varying degree of one-electron character of the transition; thus, it captures leading trends in one-electron interstate properties (i.e., when ∥γ∥ is small, the respective interstate matrix elements are also small). However, finer variations in properties that arise due to the dependence of the matrix elements of the respective operators may not be reproduced. Analysis of NACs in ethylene dimer reveals that intermolecular components of NACs follow the trends in ∥γ∥ well, as they are determined primarily by the characters of the two wave functions; however, intramolecular components depend on the relative orientation of the two moieties via the dependence in the derivative of the electron-nuclear Coulomb operator. Therefore, intramolecular NACs may exhibit large variations even when the changes in ∥γ∥ are small. We observe large NACs at perfectly stacked geometry; however, larger values (by a factor of 1.6) are observed at slip-stacked (along the long axis) geometries. Larger values of NACs at slip-stacked configurations are due to the breaking of symmetry of the local environment of the heavy atoms and not due to the wave function composition. We found that the variations in ∥γ∥ for ethylene dimer are due to a varying admixture of the charge-resonance configurations in the S1 state, whereas the (1)ME state retains its pure multiexciton character.