Molecular Isomerization Research Articles

Isomerism in Titanium‐Oxo Clusters: Molecular Anatase Model with Atomic Structure and Improved Photocatalytic Activity

AbstractPhase isomerism is a common and important phenomenon in inorganic materials, but the molecular isomerism of their nanocluster models is still rare. In this work, we report the first pair of isomeric titanium‐oxo clusters. Through combining pentagonal {Ti(Ti5)} building units in corner‐sharing or edge‐sharing forms, the two obtained Ti20‐oxo clusters take vertical and horizontal core configurations, respectively, which are both functionalized by the same organic ligands. More interestingly, the vertical type Ti20‐oxo core contains an identical {Ti8O14} moiety as anatase, making it the first molecular model of anatase TiO2. As a result, the vertical type cluster exhibits better photocatalytic H2 evolution activity, higher photocurrent response and faster charge transfer to external acceptors than its horizontal isomer. Thus, this work provides a cluster isomer method to understand the structure–property relationship of import titanium oxide materials.

Re- and Preconfigurable Multistable Visible Light Responsive Surface Topographies.

Light responsive materials that are able to change their shape are becoming increasingly important. However, preconfigurable bistable or even multi-stable visible light responsive coatings have not been reported yet. Such materials will require less energy to actuate and will have a longer lifetime. Here, it is shown that fluorinated azobenzenes can be used to create rewritable and pre-configurable responsive surfaces that show multi-stable topographies. These surface structures can be formed and removed by using low intensity green and blue light, respectively. Multistable preconfigured surface topographies can also be created in the absence of a mask. The method allows for full control over the surface structures as the topographical changes are directly linked to the molecular isomerization processes. Preliminary studies reveal that these light responsive materials are suitable as adaptive biological surfaces.

Thermally-induced reversible structural isomerization in colloidal semiconductor CdS magic-size clusters

Structural isomerism of colloidal semiconductor nanocrystals has been largely unexplored. Here, we report one pair of structural isomers identified for colloidal nanocrystals which exhibit thermally-induced reversible transformations behaving like molecular isomerization. The two isomers are CdS magic-size clusters with sharp absorption peaks at 311 and 322 nm. They have identical cluster masses, but slightly different structures. Furthermore, their interconversions follow first-order unimolecular reaction kinetics. We anticipate that such isomeric kinetics are applicable to a variety of small-size functional nanomaterials, and that the methodology developed for our kinetic study will be helpful to investigate and exploit solid–solid transformations in other semiconductor nanocrystals. The findings on structural isomerism should stimulate attention toward advanced design and synthesis of functional nanomaterials enabled by structural transformations.

Electron Density Analysis of Metal Clusters with Semi-Interstitial Main Group Atoms. Chemical Bonding in [Co6X(CO)16]- Species.

In this work, we propose a careful and thorough analysis of the chemical bond nature in high nuclearity metal carbonyl clusters having semi-interstitial main group atoms. We investigated the species [Co6X(CO)16]- (X = As, P), known for a rather interesting conformational flexibility of the cluster (leading to open or closed cages) and a corresponding polymorphism in the solid state (observed at least for X = As). The factors that trigger the molecular isomerism and the nature of X-Co and Co-Co interactions emerge from theoretical calculations and high resolution X-ray diffraction. Both energy and charge density atomic partitioning (QTAIM, EDA, IQA) are employed for this analysis, with the aim of revealing the stabilizing/destabilizing factors of the interaction between the cage and the semi-interstitial atoms in the various conformations.

Excited-state properties of the central-cis isomer of the carotenoid peridinin

The central-cis isomer of the carotenoid peridinin, presumably 13-cis, was separated and studied with spectroscopic methods including static absorption, fluorescence and femtosecond time-resolved absorption. The investigations exposed differences in the photophysical properties of this isomer in respect to all-trans peridinin. Steady-state absorption spectroscopy revealed the presence of an additional weak absorption band at the long wavelength tail of the main S0 → S2 transition. Modelling of the hypothetical vibronic progression of the S0 → S1 electronic transition demonstrated that this weak band can be associated with a higher (0–2) vibronic band of the transition and that lower vibronic bands have negligible intensities due to a large displacement between the S0 and S1 states energy curves as also suggested by the spectral shape of steady-state fluorescence emission. Transient absorption studies demonstrated that the lifetime of the S1 state of the central-cis isomer is shorter compared to the all-trans counterpart by 6–16%, depending on the polarity of the solvent. On the other hand, molecular isomerization negligibly affects the lifetime of intramolecular charge transfer (ICT), which for both isomers is ∼10 ps in the polar solvent methanol.

Reversible Modulation of Elasticity in Fluoroazobenzene-Containing Hydrogels Using Green and Blue Light.

Hydrogels are soft materials that have found multiple applications in biomedicine and represent a good platform for the introduction of molecular switches and synthetic machines into macromolecular networks. Tuning their mechanical properties reversibly with light is appealing for a variety of advanced applications and has been demonstrated in the past; however, their activation typically requires the use of UV light, which displays several drawbacks related to its damaging character and limited penetration in tissues and materials. This study circumvents this limitation by introducing all-visible ortho-fluoroazobenzene switches into a hydrophilic network, which, as a result, can be activated with green or blue light. Photoisomerization of the photochromic moieties is accompanied by a reversible tuning of the elastic modulus. The translation of molecular isomerization within the network into macroscopic modulation of its mechanical properties is attributed to different aggregation tendencies of the E and Z isomers of the azobenzene derivatives.

Molecular Isomerization and Multiscale Phase Transitions of a Ditopic Ligand on a Surface

A multiscale irreversible phase transition of a ditopic ligand on a surface has been investigated by scanning tunneling microscopy. The phase transitions, which are generated by protonation, involve an intramolecular cis- to trans-like isomerization, a change from weak to strong hydrogen bonding, and a structural phase transformation of gear chains into a stripe-like organization.

A Biologically-validated HCV E1E2 Heterodimer Structural Model

The design of vaccine strategies and the development of drugs targeting the early stages of Hepatitis C virus (HCV) infection are hampered by the lack of structural information about its surface glycoproteins E1 and E2, the two constituents of HCV entry machinery. Despite the recent crystal resolution of limited versions of both proteins in truncated form, a complete picture of the E1E2 complex is still missing. Here we combined deep computational analysis of E1E2 secondary, tertiary and quaternary structure with functional and immunological mutational analysis across E1E2 in order to propose an in silico model for the ectodomain of the E1E2 heterodimer. Our model describes E1-E2 ectodomain dimerization interfaces, provides a structural explanation of E1 and E2 immunogenicity and sheds light on the molecular processes and disulfide bridges isomerization underlying the conformational changes required for fusion. Comprehensive alanine mutational analysis across 553 residues of E1E2 also resulted in identifying the epitope maps of diverse mAbs and the disulfide connectivity underlying E1E2 native conformation. The predicted structure unveils E1 and E2 structures in complex, thus representing a step towards the rational design of immunogens and drugs inhibiting HCV entry.

Molecular isomerism induced Fe(ii) spin state difference based on the tautomerization of the 4(5)-methylimidazole group.

Two iron(ii) molecular isomers, namely face-Λ-[Fe(L1)3](ClO4)2 (1a) (L1 = R-1-phenyl-N-((1-hexyl-5-methyl-1H-imidazol-2-ylmethylene)ethanamine)) and face-Λ-[Fe(L2)3](ClO4)2 (1b) (L2 = R-1-phenyl-N-(1-hexyl-4-methyl-1H-imidazol-2-ylmethylene)ethanamine), are obtained via a well-designed strategy based on the tautomerization of the 4(5)-methylimidazole group. Structural investigations reveal that the two isomers are extremely similar with only differences in the methyl group position of the ligands. The iron(ii) center is surrounded by three bidentate imidazole Schiff-base ligands in the face-Λ conformation, which affords a distorted [FeN6] octahedral coordination sphere. The average Fe-N bond length of 1a (1.971 Å) is shorter than that of 1b (2.185 Å). Spectroscopy analyses, X-ray crystal structures and magnetic investigations show that 1a is in the low-spin state at room temperature due to the strong ligand field imparted by the electron-donating methyl groups at the 5-position on the imidazole moieties and undergoes a partial spin transition with an estimated T1/2 = 390 K. In contrast, 1b is stabilized in the high-spin state because of the strong steric hindrance when the three methyl "legs" are changed from the 5-position to the 4-position on the imidazole moieties. In addition, a new complex, 2, without methyl groups attached to the imidazole rings is introduced and characterized to further corroborate the steric influence on the spin state. Complex 2 exhibits a gradual spin-crossover behaviour with T1/2 = 258 K. Moreover, the diverse spin states of these complexes are computationally studied using the DFT method. The results of the calculations are consistent with the experiments, which prove that the competition of the electronic effect and steric crowding influence the spin states.

Isomerization-induced introduction of metal cations into polyoxomolybdate-surfactant hybrid crystals

Monovalent metal cations (Ag+, K+, and Cs+) were successfully introduced into inorganic-organic hybrid crystals composed from β-type octamolybdate (β-Mo8) and hexadecylpyridinium (C16py). The introduction of metal cations was induced by the molecular isomerization from α-Mo8 to β-Mo8 anion. All hybrid crystals consisted of alternate stacking of β-Mo8 inorganic and C16py organic layers. In the inorganic layers, the metal cations and β-Mo8 anions were connected to form one- or two-dimensional arrangement, which depended on the ionic radius of metal cations.

A green protocol for efficient discovery of novel natural compounds: Characterization of new ginsenosides from the stems and leaves of Panax ginseng as a case study

Exploration of new natural compounds is of vital significance for drug discovery and development. The conventional approaches by systematic phytochemical isolation are low-efficiency and consume masses of organic solvent. This study presents an integrated strategy that combines offline comprehensive two-dimensional liquid chromatography, hybrid linear ion-trap/Orbitrap mass spectrometry, and NMR analysis (2D LC/LTQ-Orbitrap-MS/NMR), aimed to establish a green protocol for the efficient discovery of new natural molecules. A comprehensive chemical analysis of the total ginsenosides of stems and leaves of Panax ginseng (SLP), a cardiovascular disease medicine, was performed following this strategy. An offline 2D LC system was constructed with an orthogonality of 0.79 and a practical peak capacity of 11,000. The much greener UHPLC separation and LTQ-Orbitrap-MS detection by data-dependent high-energy C-trap dissociation (HCD)/dynamic exclusion were employed for separation and characterization of ginsenosides from thirteen fractionated SLP samples. Consequently, a total of 646 ginsenosides were characterized, and 427 have not been isolated from the genus of Panax L. The ginsenosides identified from SLP exhibited distinct sapogenin diversity and molecular isomerism. NMR analysis was finally employed to verify and offer complementary structural information to MS-oriented characterization. The established 2D LC/LTQ-Orbitrap-MS/NMR approach outperforms the conventional approaches in respect of significantly improved efficiency, much less use of drug materials and organic solvent. The integrated strategy enables a deep investigation on the therapeutic basis of an herbal medicine, and facilitates new compounds discovery in an efficient and environmentally friendly manner as well.

Coherent coupling of molecular resonators with a microcavity mode.

The optical hybridization of the electronic states in strongly coupled molecule–cavity systems have revealed unique properties, such as lasing, room temperature polariton condensation and the modification of excited electronic landscapes involved in molecular isomerization. Here we show that molecular vibrational modes of the electronic ground state can also be coherently coupled with a microcavity mode at room temperature, given the low vibrational thermal occupation factors associated with molecular vibrations, and the collective coupling of a large ensemble of molecules immersed within the cavity-mode volume. This enables the enhancement of the collective Rabi-exchange rate with respect to the single-oscillator coupling strength. The possibility of inducing large shifts in the vibrational frequency of selected molecular bonds should have immediate consequences for chemistry.

Novel pentablock copolymer-based nanoparticulate systems for sustained protein delivery.

The design, synthesis, and application of novel biodegradable and biocompatible pentablock (PB) copolymers, i.e., polyglycolic acid-polycaprolactone-polyethylene glycol-polycaprolactone-polyglycolic acid (PGA-PCL-PEG-PCL-PGA) and polylactic acid-polycaprolactone-polyethylene glycol-polycaprolactone-polylactic acid (PLA-PCL-PEG-PCL-PLA) for sustained protein delivery, are reported. The PB copolymers can be engineered to generate sustained delivery of protein therapeutics to the posterior segment of the eye. PB copolymers with different block arrangements and molecular weights were synthesized by ring-opening polymerization and characterized by proton nuclear magnetic resonance ((1)H-NMR), gel permeation chromatography (GPC), and X-ray diffraction (XRD) spectroscopy. Immunoglobulin G (IgG) was selected as a model protein due to its structural similarity to bevacizumab. The influence of polymer molecular weight, composition, and isomerism on formulation parameters such as entrapment efficiency, drug loading, and in vitro release profile was delineated. Crystallinity and molecular weight of copolymers exhibited a substantial effect on formulation parameters. A secondary structure of released IgG was confirmed by circular dichroism (CD) spectroscopy. In vitro cytotoxicity, cell viability, and biocompatibility studies performed on human retinal pigment epithelial cells (ARPE-19) and/or macrophage cell line (RAW 264.7) demonstrated PB copolymers to be excellent biomaterials. Novel PB polymers may be the answer to the unmet need of a sustained release protein formulation.

Deformation-Induced Structural Transformations in Molecular Crystals

The physical mechanisms of the deformation-induced structural transformations in molecular crystals, including morphological changes, amorphization and molecular polymorphous conversions in nano-dispersed bioinorganic compounds are discussed in this work. Integrated study using direct structural and structure-sensitive spectroscopic methods allowed obtaining the data on polymorphous transformations, taking place during mechanical activation in calcium gluconate monohydrate (CG). One of the possible reasons for lattice polymorphous transformations and amorphization, observed in the course of mechanical activation of low-symmetry molecular crystals, might be the spatial molecular isomerization. In this case, the disappearance of the translational invariance of the lattice is conditioned by the simultaneous coexistence of the reactants and reaction products, which have di erent stereoorganization of the molecular structure.

Three-Pulse ELDOR Theory Revisited

The current theory of three-pulse electron double resonance (PELDOR) has been generalized to the case, when paramagnetic particles (spin labels) in pairs or groups have the electron paramagnetic resonance (EPR) spectra, which overlap essentially or coincide. The PELDOR signal modulation induced by the dipole–dipole interaction between paramagnetic spin ½ particles in pairs embedded in disordered systems has been analyzed comprehensively. It has been shown that the PELDOR signal contains additional terms in contrast to the situation considered in the current theory, when the EPR spectra of the spin labels in the pairs do not overlap. In disordered systems, the pairs of spin labels have the characteristic dipolar interaction frequency. According to the current theory for pairs of spin labels, the PELDOR signal reveals the modulation with this characteristic frequency. The additional terms, which are obtained in this work, do not change the modulation frequency of the PELDOR signal for pairs of spin labels. However, these additional terms should be taken into account when analyzing the amplitude of the PELDOR signal and the amplitude of the modulation of the PELDOR signal. The consistent approach to treating the PELDOR data for the groups containing three or more spin labels has been outlined on the basis of the results for pairs of spin labels. It has been also analyzed how the spin flips and molecular motion or molecular isomerization can affect the manifestation of the interaction between the spin labels in PELDOR experiments. PELDOR experiments for the stable biradicals (biradicals I containing 1-oxyl-2,2,5,5-tetramethylpyrroline-3-yl spin labels and biradicals II containing 3-imidazoline spin labels) have been performed. The results have been interpreted within the theory developed in this work.

Molecular isomerization and fragmentation of polyatomic molecules controlled by inner-valence recollision-ionization

Control over various fragmentation reactions of a series of polyatomic molecules (acetylene, ethylene, 1,3-butadiene) by the optical waveform of intense few-cycle laser pulses is demonstrated experimentally. We show both experimentally and theoretically that the responsible mechanism is inelastic ionization from inner-valence molecular orbitals by recolliding electron wave packets.

Effect of molecular structural isomers in thermal lens spectroscopy

We explore the importance of molecular structure on thermal lens (TL) spectroscopy by measuring the effects of molecular isomerization on TL measurements. In particular, we present a case study for all the structural isomers of butanol, namely, normal-butanol (n-BuOH), secondary-butanol (s-BuOH), iso-butanol (i-BuOH) and tertiary-butanol (t-BuOH). We argue that the molecular isomerization influences the heat convection process in two possible ways: one being a change in the molecular surface area and the other being the steric hindrance. We show that n-BuOH has the highest capability to transfer heat by convection. Branching in the molecular structure renders the system sluggish as it makes the molecular motion successively retarded due to an increase in the mean free path. This we have defined as the molecular drift that slows under thermal conditions. In our studied isomers, therefore, t-BuOH drifts the slowest.

Molecular structure and linkage isomerization in copper(II) complexes containing N,N-dialkyl-N′-benzylethylenediamine and thiocyanate ligands: a combined crystallographic, spectroscopic and DFT study

A combined experimental and computational study of three thiocyanate-Cu(II) complexes with general formula [Cu(Ln)2(NCS)]ClO4, (L1 = N,N-dimethyl,N′-benzyl-ethylenediamine, L2 = N,N-diethylyl,N′-benzyl-ethylenediamine, L3 = N,N-diisopropylyl,N′-benzyl-ethylenediamine) was carried out. The compounds were synthesized and structurally characterized by physico-chemical and spectroscopic methods. X-ray crystallography of [Cu(L1)2(NCS)]ClO4 showed that the copper atom achieves a distorted square pyramidal environment through coordination of four amine N atoms and a N atom of the terminal SCN− ion. To investigate the effect of steric crowding on the coordination mode of thiocyanate at the copper(II) center, DFT calculations are carried out on the complexes. Two different cases were considered, namely when nitrogen is the donor atom and when sulfur is the donor atom. In all cases, the N-coordinated isomers were always more stable than the S-coordinated ones. The electronic spectra of the complexes were analyzed and assigned by means of DFT/TD-DFT, together with molecular orbital analysis.

Orthogonally modulated molecular transport junctions for resettable electronic logic gates.

Individual molecules have been demonstrated to exhibit promising applications as functional components in the fabrication of computing nanocircuits. Based on their advantage in chemical tailorability, many molecular devices with advanced electronic functions have been developed, which can be further modulated by the introduction of external stimuli. Here, orthogonally modulated molecular transport junctions are achieved via chemically fabricated nanogaps functionalized with dithienylethene units bearing organometallic ruthenium fragments. The addressable and stepwise control of molecular isomerization can be repeatedly and reversibly completed with a judicious use of the orthogonal optical and electrochemical stimuli to reach the controllable switching of conductivity between two distinct states. These photo-/electro-cooperative nanodevices can be applied as resettable electronic logic gates for Boolean computing, such as a two-input OR and a three-input AND-OR. The proof-of-concept of such logic gates demonstrates the possibility to develop multifunctional molecular devices by rational chemical design.

Influence of Molecular Isomerism of Monopyridylporphyrin on Electrochemical and Electrocatalytic Properties in Alkaline Solution

The comparative investigation of the electrochemical reduction of a number of pyridylporphyrin derivatives with alkyl substituents and their cobalt(II) complexes in 0.1 M KOH is carried out by cyclic voltammetry (CV). The influence of isomerism of the porphyrin molecule and the nature of metal on the oxidative capacity of the tetrapyrrole macrocycle and on the electrocatalytic activity of compounds studied for the oxygen electroreduction reaction is established.