Changes In Molecular Arrangement Research Articles

High pressure study of hydrogen-bonded energetic material 4-nitropyrazole

The study investigates the structural stability of the hydrogen-bonded energetic material 4-nitropyrazole (4-NP, C3H3N3O2) from ambient pressure to 10 GPa at room temperature using diamond anvil cell (DAC) and Raman spectroscopy. Based on the changes observed in the high-pressure Raman spectra, it is proposed that the hydrogen-bonded energetic material 4-NP undergoes a phase transition within the pressure range of 2.7–6.4 GPa. Upon complete pressure release from 10 GPa, the resulting spectrum is consistent with the Raman spectrum observed under ambient pressure, indicating that the phase transition is reversible. Ab initio calculations were used to explain the changes in molecular arrangements and hydrogen-bonded networks. Hirshfeld surfaces and fingerprint plots were used to directly compare the variations in packing patterns and intermolecular interactions. Based on the experimental and calculated results, it is proposed that the phase transition of 4-NP was likely caused by the rearrangements of the hydrogen-bonded networks.

The Impact of Molecular Packing on Organic Room Temperature Phosphorescence and Corresponding Stimulus Response Effect

AbstractOrganic luminescent materials exhibiting persistent room temperature phosphorescence (RTP) have garnered considerable interest due to their versatile applications. However, the mechanism is still unclear, especially for the molecular structure‐molecular arrangement‐property relationship. Herein, six derivatives of phenothiazine 5,5‐dioxide are synthesized, revealing their distinct RTP properties and the associated underlying mechanisms. Careful analyses of their single crystal structures, combined with initial theoretical calculations, indicate that the persistent RTP effect is facilitated by effective intermolecular π–π interactions in the solid state led by folded conformation. Specifically, PTZO‐CF3‐3F exhibits distinctive photo‐activated phosphorescence both in crystal and grinding state in response to the changes of molecular arrangement. Besides, a porous structure is found to be present in PTZO‐CF3‐2F crystal, offering it great sensitivity to oxygen for both RTP intensity and lifetime. Accordingly, the visual oxygen warning device is fabricated successfully. Furthermore, PTZO‐CF3‐3F with photo‐activated RTP effect in a grinding state is successfully utilized in the applications of anti‐counterfeiting and optical logic gates, expanding the scope of stimulus‐responsive phosphorescence materials for broader applications.

Investigating the pH dependence of thermal signatures in monohydric and polyhydric alcohols using time-resolved thermal lens spectroscopy

We study the influence of pH on the thermophysical properties of monohydric and polyhydric alcohols through a femtosecond laser-induced thermal lens (TL) spectroscopic technique. Relative changes in the thermal signatures of monohydric and polyhydric alcohols are identified at different pH levels using both dual-beam Z-scan and time-resolved TL measurements. We found the TL signatures of the alcohols not to be affected in the acidic region, but a significant change is noticed in the alkaline environment. It is observed that in an alkaline environment (pH > 7), the TL signal significantly increases for short-chain (MeOH and EtOH) monohydric alcohols. In contrast, the TL signal for longer chain length monohydric alcohols (HxOH and phenol) and polyhydroxy alcohols (Ethylene glycol & Glycerol) fall enormously. These results depend strongly on the molecular characteristics of solvents and their interaction strength with the solute as a function of changing pH strength. Our results show the influence of pH on the natural drifting and the heat dissipation characteristics of solvent molecules, which prominently participate in changing the TL signatures of samples. This event could be attributed to changes in molecular arrangements by developing solvation shells (through ions-solvents interactions) in the systems. We investigate the influence of various factors, namely, chain length, structure, polarity, and inter or the intra-H-bonding ability of solvent molecules and ion concentration, which effectively alter the solute-solvent interaction strengths at different pH values (especially in an alkaline environment). The findings through our TL measurements explore this event in great detail for the first time. We try to correlate the molecular characteristics and its ions-solvent interaction effects with the thermophysical properties of alcohols.

Multi-stimuli-responsive fluorescence switching from a novel organic polymorphic benzoimido-benzamide derivative

A novel organic polymorphic luminogen, (Z)-N-((benzoylimino) (4-(diphenylamino)phenyl)methyl)-N-(4-fluorophenyl)benzamide (DPA-PYZ-F), has been designed and synthesized successfully by a green photo-oxidation reaction. Two polymorphs (FB and FG) based on DPA-PYZ-F with different conformations display blue and green fluorescence, respectively. The emission of the newly obtained polymorphic molecule can be switched through the response to a mechanical force, thermal stimulus and protonic acid. The photophysical property tests and single crystal structural analysis disclosed that the mechanical force stimuli-responsive behavior of the FB and FG samples originate from the change of molecular arrangement. More significantly, FT-IR spectroscopy confirmed that the conformation transition from the FG to the FB could be achieved by thermal stimulus at 430 K. Additionally, protonation−deprotonation of the benzoylimino moieties in DPA-PYZ-F induced a remarkable fluorescence on-off characteristics upon protonic acid and thermal stimulus. The multi-stimuli response performance endows the new kind of molecule with the potential as a candidate for applications in mechanical force, thermal and protonic acid sensing.

POLArIS, a versatile probe for molecular orientation, revealed actin filaments associated with microtubule asters in early embryos

Biomolecular assemblies govern the physiology of cells. Their function often depends on the changes in molecular arrangements of constituents, both in the positions and orientations. While recent advancements of fluorescence microscopy including super-resolution microscopy have enabled us to determine the positions of fluorophores with unprecedented accuracy, monitoring the orientation of fluorescently labeled molecules within living cells in real time is challenging. Fluorescence polarization microscopy (FPM) reports the orientation of emission dipoles and is therefore a promising solution. For imaging with FPM, target proteins need labeling with fluorescent probes in a sterically constrained manner, but because of difficulties in the rational three-dimensional design of protein connection, a universal method for constrained tagging with fluorophore was not available. Here, we report POLArIS, a genetically encoded and versatile probe for molecular orientation imaging. Instead of using a direct tagging approach, we used a recombinant binder connected to a fluorescent protein in a sterically constrained manner that can target specific biomolecules of interest by combining with phage display screening. As an initial test case, we developed POLArISact, which specifically binds to F-actin in living cells. We confirmed that the orientation of F-actin can be monitored by observing cells expressing POLArISact with FPM. In living starfish early embryos expressing POLArISact, we found actin filaments radially extending from centrosomes in association with microtubule asters during mitosis. By taking advantage of the genetically encoded nature, POLArIS can be used in a variety of living specimens, including whole bodies of developing embryos and animals, and also be expressed in a cell type/tissue specific manner.

The initial attempt to reveal the emission processes of both mechanoluminescence and room temperature phosphorescence with the aid of circular dichroism in solid state

A phenothiazine derivative PtzChol containing non-conjugated chiral cholesterol group was designed and synthesized. By analyzing the single crystal structure of PtzChol carefully, coupled with the circular dichroism (CD) signals before and after grinding, it was found that the introduction of cholesterol produced a positive effect on the production of chiral space group, on mechanoluminescence (ML) and room temperature phosphorescence (RTP), and throughout the entire light-emitting process, the CD signal could well reflect the changes of molecular arrangement.

(Invited) Luminescent Mechanochromic Gold Complex Exhibiting Phase Transition Between Crystalline Phases

Mechanochromic luminescence is referred to as solid-state emission color changes upon mechanical stimulation, i.e., grinding, pressing and ball-milling. For mechanochromic compounds, changes in molecular arrangement and noncovalent bonding interactions patterns take place upon mechanical stimulation, and these changes resulted in the switching of photoluminescence property of mechanochromic compounds. These materials are applicable to diplays, force-sensors, memory devices, and etc. One of the pioneering mechanochromic compounds was reported in 2005, and more than 500 reports have been known for this research field in the past ten years. However, the research on luminescent mechanochromic compounds still depend on serendipitous discoveries and derivatization of known mechanochromic compounds. This is caused by the absence of rational design strategies of the mechanochromic compounds. One reason for the absence of the rational design is resulted from the fact that most mechanochromic compounds so far have shown crystal-to-amorphous phase transition. These mechanochromic materials are unfavorable for the determination of the mechanism of emission color changes upon grinding. Few mechanochromic compounds have been reported to exhibit crystal-to-crystal phase transitions. In this case, a deeper insight into structure–property relationship can be obtained, which can lead to establish the rational design/functionalization strategies of mechanochromic compounds. So far, our group have investigated luminescent mechanochromism of a series of aryl gold isocyanide complexes and reported various unique mechanochromic properties. Although we reported various gold complexes exhibiting prominent mechanochromism, it is still challenging for us to construct the mechanochromic compounds with desired functionality. Here, we will report a novel “screening approach” to establish mechanochromic compounds exhibiting a crystal-to-crystal phase transition. In this approach we first prepared 48 para-substituted (R1) phenyl[para-substituted (R2) phenyl isocyanide]gold(I) complexes R1 - R2 (six kinds of R1 and eight R2 substituents). For these 48 complexes, we then performed three-step screening experiments. The first screening experiment was focus on selection of emissive R1 - R2 complexes under UV light. This experiment gave 37 emissive R1 - R2 complexes. For these 37 R1 - R2 complexes, the second screening experiment was performed where the luminescent mechanochromic behaviors were evaluated through emission spectroscopy. Then, we identified 28 mechanochromic complexes. As the third screening experiment, we evaluated mechano-induced changes in the powder diffraction patterns of 28 complexes. Then, we newly found CF3 - CN exhibited a crystal-to-crystal phase transition upon mechanical stimulation. We also successfully prepared two distinct single crystals of CF3 - CN corresponding to mechanically unprocessed and processed phases. Theoretical calculations indicated that the red-shifted emission of CF3 - CN in response to mechanical stimulation is caused by the formation of aurophilic interactions. Figure 1

Pressure-Induced Reversible Amorphization in Hydrogen-Bonded Crystalline Phenyl Carbamate Form-I

We characterized the high-pressure response of hydrogen-bonded crystalline phenyl carbamate (C7H7NO2, PC) form-I through in situ synchrotron X-ray diffraction (XRD) and Raman spectroscopy in a diamond anvil cell (DAC) under pressures of up to ∼13 GPa at room temperature. No evidence for the polymorphic transformation of crystalline PC form-I crystal to form-II was observed under high pressure. The evolution of the XRD patterns and Raman spectra indicated that crystalline PC form-I underwent reversible pressure-induced amorphization (PIA) at 12.7 GPa. Ab initio calculations were performed to account for the changes in molecular arrangements and hydrogen-bonded networks in PC form-I under pressure. Hirshfeld surfaces and fingerprint plots were utilized to directly compare the variations in packing patterns and intermolecular interactions. Based on the experimental and calculated results, we proposed that PIA in crystalline PC form-I is driven by the competition between close packing and long-range order. Thi...

Influence of thermocleavable functionality on organic field-effect transistor performance of small molecules

Diketopyrrolopyrrole based donor-acceptor-donor conjugated small molecules using ethylene dioxythiophene as a donor was synthesized. Electron deficient diketopyrrolopyrrole unit was substituted with thermocleavable (tert-butyl acetate) side chains. The thermal treatment of the molecules at 160°C eliminated the tert-butyl ester group results in the formation of corresponding acid. Optical and theoretical studies revealed that the molecules adopted a change in molecular arrangement after thermolysis. The conjugated small molecules possessed p-channel charge transport characteristics in organic field effect transistors. The charge carrier mobility was increased after thermolysis of tert-butyl ester group to 5.07×10−5cm2/Vs.

Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals.

Two-dimensional (2D) crystalline materials possess unique structural, mechanical, and electronic properties1,2, which have rendered them highly attractive in many applications3-5. Although there have been advances in preparing 2D materials that consist of one or few atomic/molecular layers6,7, bottom-up assembly of 2D crystalline materials remains a considerable challenge and an active area of development8-10. Even more challenging is the design of dynamic 2D lattices that can undergo large-scale motions without loss of crystallinity. Dynamicity in porous 3D crystalline solids has been exploited for stimuli-responsive functions and adaptive behavior11-13. As in the case of such 3D materials, integrating flexibility/adaptiveness into crystalline 2D lattices would greatly broaden the functional scope of 2D materials. Here we report the self-assembly of unsupported, 2D protein lattices with precise spatial arrangements and patterns through a readily accessible design strategy. Three single- or double-point mutants of the C4 symmetric protein RhuA were designed to assemble via different modes of intermolecular interactions (single disulfide, double disulfide and metal coordination) into crystalline 2D arrays. Owing to the flexibility of the single disulfide interactions, the lattices of one of the variants (C98RhuA) are essentially defect-free and undergo substantial but fully correlated changes in molecular arrangement, giving coherently dynamic 2D molecular lattices. Notably, C98RhuA lattices possess a Poisson's ratio of −1, the lowest thermodynamically possible value for an isotropic material.

Characterization of solid polymer dispersions of active pharmaceutical ingredients by 19F MAS NMR and factor analysis

In this contribution the ability of 19F MAS NMR spectroscopy to probe structural variability of poorly water-soluble drugs formulated as solid dispersions in polymer matrices is discussed. The application potentiality of the proposed approach is demonstrated on a moderately sized active pharmaceutical ingredient (API, Atorvastatin) exhibiting extensive polymorphism. In this respect, a range of model systems with the API incorporated in the matrix of polvinylpyrrolidone (PVP) was prepared. The extent of mixing of both components was determined by T1(1H) and T1ρ(1H) relaxation experiments, and it was found that the API forms nanosized domains. Subsequently it was found out that the polymer matrix induces two kinds of changes in 19F MAS NMR spectra. At first, this is a high-frequency shift reaching 2–3ppm which is independent on molecular structure of the API and which results from the long-range polarization of the electron cloud around 19F nucleus induced by electrostatic fields of the polymer matrix. At second, this is broadening of the signals and formation of shoulders reflecting changes in molecular arrangement of the API. To avoid misleading in the interpretation of the recorded 19F MAS NMR spectra, because both the contributions act simultaneously, we applied chemometric approach based on multivariate analysis. It is demonstrated that factor analysis of the recorded spectra can separate both these spectral contributions, and the subtle structural differences in the molecular arrangement of the API in the nanosized domains can be traced. In this way 19F MAS NMR spectra of both pure APIs and APIs in solid dispersions can be directly compared. The proposed strategy thus provides a powerful tool for the analysis of new formulations of fluorinated pharmaceutical substances in polymer matrices.

Hydrogen Bonding and Molecular Rearrangement in 1,3,5-Triamino-2,4,6-trinitrobenzene under Compression

We studied the structural behavior and properties of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) under hydrostatic compression using atomistic and electronic (ab initio) level computations. We observed a marked change in the intermolecular hydrogen-bonding network upon compression of the crystal without change in crystal symmetry. The changes in molecular arrangement are found to have a profound impact on various observable properties: energetic, vibrational spectra, structural, and elastic properties. From the analysis of vibrational modes, we observed that the changes are mainly due to the nitro and amino groups. An increase in the number of hydrogen bonding interactions along the c-axis of the crystals results in providing the extra stabilization energy. In addition to analyze the isolated molecule and dimer, this molecular rearrangement is systematically studied and characterized in the condensed phase. From higher-level ab initio calculations, the potential energy surface of the dimer indicates the presence of a region with two local minima within 3.42 kcal/mol difference in energy. Since this behavior is not associated with a change of symmetry of the crystal unit cell, the possible coexistence of two molecular arrangements might lead to the loss of a definitive inversion center for bulk. The calculated elastic constants of the crystal dramatically reveal the changes via large increases in certain components. Implications on the observed pressure-induced rearrangement behavior on the mechanical, optical, and thermodynamic properties of TATB are further discussed, and correlations with experimental spectroscopic data are provided.

Mechanofluorochromism of a Series of Benzofuro[2,3‐c]oxazolo[4,5‐a]carbazole‐Type Fluorescent Dyes

AbstractMechanofluorochromism is found for a series of benzofuro[2,3‐c]oxazolo[4,5‐a]carbazole‐type fluorophores (1a–1d) having cyano groups as acceptor: grinding of 1a–1d induces a fluorescent color change with an enhanced quantum yield, and the fluorescent color is recovered by heating or exposure to solvent vapor. Interestingly, both absorption and emission peaks are redshifted by grinding, in conflict with the common view. On the basis of time‐resolved fluorescence spectroscopy, X‐ray powder diffraction (XRD), differential scanning calorimetry (DSC), and single‐crystal X‐ray structural analysis, the mechanofluorochromism observed with this new class of fluorescent dyes is found to accompany a reversible switching between crystalline and amorphous states with changes of molecular arrangement and intermolecular π–π interactions. An essential role of a strong donor‐π‐acceptor character of the dyes is pointed out for the manifestation of the observed mechanofluorochromism.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

Change in Molecular Orientation with Condensation of 4,4′-Bis(trihydroxysilyl)biphenyl Crystals

Abstract Molecular orientation in 4,4′-bis(trihydroxysilyl)biphenyl plate-like square crystals (BPSi) and orientation change with heating-induced condensation were investigated using polarization optical microscopy. The biphenylylene groups in BPSi were arranged along a diagonal of the square plane with a tilt angle of 21° from the planar normal. This arrangement was maintained up to 200 °C for several minutes, but heating at 250 °C promoted a condensation reaction which formed siloxane bonds, causing changes in molecular orientation to a tilt angle of 0°, and altering the shape of BPSi crystals from square to rhombic. The molecular arrangement and its change after condensation were qualitatively confirmed by molecular-mechanics simulation. The absorption and fluorescence bands of the biphenylylene groups were significantly red-shifted by the condensation due to the change in molecular arrangement, which resulted from a notable decrease in biphenylylene–biphenylylene separation.

Study of the dynamics of surface molecules by time-resolved sum-frequency generation spectroscopy

Sum-frequency generation (SFG) is a nonlinear laser-spectroscopy technique suitable for analysis of adsorbed molecules. The sub-monolayer sensitivity of SFG spectroscopy enables vibrational spectra to be obtained with high specificity for a variety of molecules on a range of surfaces, including metals, oxides, and semiconductors. The use of ultra-short laser pulses on time-scales of picoseconds also makes time-resolved measurements possible; this can reveal ultrafast transient changes in molecular arrangements. This article reviews recent time-resolved SFG spectroscopy studies revealing site-hopping of adsorbed CO on metal surfaces and the dynamics of energy relaxation at water/metal interfaces.

Consideration of molecular arrangements in regio- and enantioselective reduction of an NAD model compound controlled by carbonyl oxygen orientation

The regio- and enantioselectivity of the reduction of an NAD model compound having axial chirality with respect to the C(3)(quinolinium)-C(carbonyl) bond, 3-piperidinylcarbonyl-1,2,4-trimethylquinolinium ion (1), by using several reducing agents is described. Reaction of 1 with sodium hydrosulfite affords the 1,4-reduced product, 3-piperidinylcarbonyl-1,2,4-trimethyl-1,4-dihydroquinoline (), with low enantioselectivity, whereas sodium borohydride promotes 1,2-reduction, affording 3-piperidinylcarbonyl-1,2,4-trimethyl-1,2-dihydroquinoline () as the sole product in a moderate enantioselectivity. When 1 was reduced by the chiral NADH model compound, 2,4-dimethyl-3-(N-alpha-methylbenzylcarbamoyl)-1-propyl-1,4-dihydropyridine (Me(2)PNPH (4)), the regioselectivity and enantioselectivity of the reaction were significantly altered by the stereochemistry of 1 and 4. An achiral NADH model compound, 1-propyl-1,4-dihydronicotinamide (PNAH (5)) exhibited both high regio- and enantioselectivities. The product selectivity reflects the change in molecular arrangement in the transition state of the reaction and reveals the relative importance of the parameters governing the molecular arrangement in the reaction.

Pressure-frozen benzene I revisited

The crystal structure of benzene, C6H6, in situ pressure-frozen in phase I, has been determined by X-ray diffraction at 0.30, 0.70 and 1.10 GPa, and 296 K. The molecular aggregation within phase I is consistent with van der Waals contacts and electrostatic attraction of the positive net atomic charges at the H atoms with the negative net charges of the C atoms. The C-H...aromatic ring centre contacts are the most prominent feature of the two experimentally determined benzene crystal structures in phases I and III, whereas no stacking of the molecules has been observed. This specific crystal packing is a likely reason for the exceptionally high polymerization pressure of benzene. The changes of molecular arrangement within phase I on elevating the pressure and lowering the temperature are analogous.

The Effect of Kaolinite Intercalation on the Structural Arrangements of N-Methylformamide and 1-Methyl-2-pyrrolidone

N-methylformamide (NMF) and 1-methyl-2-pyrrolidone (NMP) were intercalated with kaolinite, characterized, and deintercalated for analysis (the NMP was intercalated after expansion of the kaolinite layers with NMF). The dynamics of guest molecules within the kaolinite lamellae was studied by means of FT-IR and liquid state 1H and 13C NMR on the NMF and NMP before intercalation and also on the deintercalated solutions. Both compounds were deintercalated using water. The FT-IR spectra show no significant differences before and after intercalation, for either NMF or NMP, indicating that there is no change in molecular arrangement as a result of intercalation. 1H and 13C NMR investigations supported the findings of the FT-IR and indicated that structural arrangement and orientation of the guest species remain the same after deintercalation. This work provides evidence that intercalation is due to weak physical bonding.

Fluorescence study on intermolecular complex formation between mesogenic terphenyldiimide moieties of a thermotropic liquid-crystalline polyimide

Intermolecular complex formation between mesogenic terphenyldiimide moieties of a thermotropic liquid-crystalline (LC) polyimide (P-11TPE) was studied by steady-state fluorescence and fluorescence lifetime measurements together with differential scanning calorimetry (d.s.c.) and wide-angle X-ray diffraction (WAXD). The P-11TPE shows various highly-ordered crystalline phases and a smectic phase during heating, according to the d.s.c. and WAXD results. By comparing the fluorescence spectra and fluorescence lifetimes between P-11TPE and its model compound ( N, N′-diundecylter-phenyldiimide), the fluorescing complex at 438 nm of P-11TPE is confirmed to be an intermolecular ground-state complex between two terphenyldiimide moieties. The fluorescence peak wavelength of this intermolecular complex shifts slightly to shorter wavelength below the glass transition temperature and shifts abruptly to longer wavelength around crystallization, then shifts gradually to shorter wavelength again from various crystalline phases until the isotropic phase. The changes in fluorescence intensity and fluorescence lifetime around phase transition temperatures are also observed. These apparent changes in fluorescence behaviour indicate the differences in the nature and number of intermolecular complexes and radiationless deactivation processes in various phases. The characteristics of fluorescence behaviour for P-11TPE are also compared to those for various LC polyesters studied previously, and it is concluded that the red shift of fluorescnece is due to the apparent change in molecular arrangement between mesogenic moieties and the blue shift of fluorescence is due to the almost identical packing pattern with increasing thermal fluctuation during phase transition for liquid crystal polymers. By using fluorescence technique, molecular interaction between mesogenic moieties of liquid crystal polymer has been proved to show various patterns of changes during phase transition processes.

Molecular-scale structures of Langmuir–Blodgett films of fatty acids observed by atomic force microscopy (II) – cation dependence

The morphologies of LB films of arachidic acid and its salt were observed by atomic force microscopy (AFM) to reveal their cation dependence from the viewpoint of ionic radius and solution pH. The salt films having divalent metal ions (Ba2+, Sr2+ and Co2+) except for Mn2+ showed similar characteristic stripe-shaped macroscopic structures. An area per molecule in the film increased with decrease of ionic radius. Concerning the solution pH, significant changes in molecular arrangements and macroscopic structures were observed in the barium arachidate films. Coexistence of 2×2 superstructures with 1×1 fundamental structures were observed at pH=8.0, but 3×1 at pH=9.8. These structures were considered to depend on the increase of the salt forming ratio increases with pH.