Dimeric Molecules Research Articles

IR Study of the Transformation of WF6 on a W Substrate

A new IR-spectroscopy (infrared) technique allowing investigation of the transformation of gaseous WF6 on a W surface heated up to 860 K in a hydrogen and argon atmosphere is proposed. The weak chemical adsorption of WF6 on W substrates is observed. The intermediate reaction products of WF6 with solid W above 670 K are penta- and tetra-tungsten fluorides. The presence of other low-valent tungsten fluorides is possible in the form of adsorbed oligomeric molecules (dimers or trimers). It is shown that low-valent tungsten fluorides are strongly adsorbed on the surface of W. The adsorbed layers formed on the W substrate in the WF6 + H2 mixture and pure WF6 str identical in composition.

Limitations of Global Hybrids in Predicting the Geometries and Torsional Energy Barriers of Dimeric Systems and the Role of Hartree Fock and DFT Exchange.

Prediction of accurate geometries is a prerequisite for accurate prediction of molecular properties. Impact of Hartree Fock (HF) exchange (a0 ) on geometry in the framework of DFT is investigated by monitoring dihedral angles, bond length alternations, and torsional energy barriers of 10 dimeric systems against CCSD (ADZ/ATZ) benchmarks. A strong correlation is observed between the fraction of HF exchange, equilibrium dihedral angles, and the potential energy barriers in global hybrids. Full HF exchange is critical to accurately predict the nonplanarity. Lower fractions of (a0 )/larger DFT exchange (1-a0 ) results in overestimation of torsional energy barriers at 900 and underestimation at 00 . Large contributions of (1-a0 ) in global hybrid functionals tend to overestimate torsional energy barriers (900 ) and are biased toward planar geometries. However, inclusion of larger fractions of (a0 )/lower (1-a0 ) also overestimate the torsional energy barriers in syn-conformations due to the localization errors associated with HF exchange in global hybrids. Hence, irrespective of the fraction of HF/DFT exchange incorporated, global hybrids fail to accurately predict torsional energy barriers at 00 and 900 simultaneously. Long-range corrected (LC) functionals, which employ full HF exchange at longer regions, outperform global hybrid functionals in predicting geometries and torsional energy barriers of the dimeric molecules. The distance dependence of (a0 ) thus provides a balanced fraction of HF exchange as the dihedral torsion varies. Impact of range separation parameter on geometries is marginal in altering the planarity/nonplanarity. However, range separation parameter within 0.20-0.40 bohr-1 predicts more reliable torsional energies and geometries. © 2019 Wiley Periodicals, Inc.

Aromaticity Suppression by Intermolecular Coordination. Optical Spectra and Electronic Structure of Heavy Carbene Analogues with an Amidophenolate Backbone

Experimental optical (UV–vis, Raman) and computational magnetic (NICS, GIMIC) criteria were used to study the aromaticity of group 14 N,O-heterocyclic carbenes tBuAPE (AP = amidophenolate, E = Ge, Sn, Pb). The UV–vis and Raman spectra of the monomeric compound with E = Ge were shown to differ significantly from those of dimeric compounds with E = Sn, Pb. The reason for these phenomena is suppression in the dimeric molecules of 10 π-electron aromaticity due to partial filling of the vacant pz orbital of the EII atom caused by intermolecular coordination N→EII. The monomeric forms of all molecules studied are aromatic according to all the criteria used.

Full quantum calculation of the rovibrational states and intensities for a symmetric top-linear molecule dimer: Hamiltonian, basis set, and matrix elements.

The rovibrational energy levels and intensities of the CH3F-H2 dimer have been obtained using our recent global intermolecular potential energy surface [X.-L. Zhang et al., J. Chem. Phys. 148, 124302 (2018)]. The Hamiltonian, basis set, and matrix elements are derived and given for a symmetric top-linear molecule complex. This approach to the generation of energy levels and wavefunctions can readily be utilized for studying the rovibrational spectra of other van der Waals complexes composed of a symmetric top molecule and a linear molecule, and may readily be extended to other complexes of nonlinear molecules and linear molecules. To confirm our method, the rovibrational levels of the H2O-H2 dimer have been computed and shown to be in good agreement with experiment and with previous theoretical results. The rovibrational Schrödinger equation has been solved using a Lanczos algorithm together with an uncoupled product basis set. As expected, dimers containing ortho-H2 are more strongly bound than dimers containing para-H2. Energies and wavefunctions of the discrete rovibrational levels of CH3F-paraH2 complexes obtained from the direct vibrationally averaged 5-dimensional potentials are in good agreement with the results of the reduced 3-dimensional adiabatic-hindered-rotor (AHR) approximation. Accurate calculations of the transition line strengths for the orthoCH3F-paraH2 complex are also carried out, and are consistent with results obtained using the AHR approximation. The microwave spectrum associated with the orthoCH3F-orthoH2 dimer has been predicted for the first time.

Photophysical Properties of Upconverting Nanoparticle-Phthalocyanine Complexes.

Interaction between upconverting nanoparticles and aluminum octacarboxyphthalocyanine was studied. The efficiency of non-radiative energy transfer from the nanoparticles to phthalocyanine increased with the number of phthalocyanine molecules adsorbed on the nanoparticle, but only up to a certain limit. Further increase in the phthalocyanine concentration resulted in a decrease of its sensitized fluorescence due to the dimerization of dye molecules on the nanoparticle surface. When subjected to infrared irradiation, phthalocyanine molecules in the hybrid complex generated singlet oxygen. The observed effects are of interest in regard to the targeted search for new components of efficient third-generation hybrid photosensitizers.

N-Bromosuccinimide-mediated dimerization of unsymmetrical indodicarbocyanine dyes

The bromination of unsymmetrical indodicarbocyanine dyes bearing electron-donating groups (–NHCOCH3, –OH) on the aryl rings using N-bromosuccinimide produces dimeric molecules together with the corresponding meso-brominated dyes. The direction of the process depends on the reaction conditions. A possible reaction mechanism is also discussed.

Photodissociation of S2 (X3Σg-, a1Δg, and b1Σg+) in the 320-205 nm Region.

Photodissociation of vibrationally and electronically excited sulfur dimer molecules (S2) has been studied in a combined experimental and computational quantum chemistry study in order to characterize bound-continuum transitions. Ab initio quantum chemistry calculations are carried out to predict the potential energy curves, spin–orbit coupling, transition moments, and bound-continuum spectra of S2 for comparison with the experimental data. The experiment uses velocity map imaging to measure S-atom production following S2 photoexcitation in the ultraviolet region (320–205 nm). A pulsed electric discharge in H2S produces ground-state S2 X3Σg–(v = 0–15) as well as electronically excited singlet sulfur and b1Σg+(v = 0, 1), and evidence is presented for the production and photodissociation of S2 a1Δg. In a previous paper, we reported threshold photodissociation of S2X3Σg–(v = 0) in the 282–266 nm region. In the present study, S(3PJ) fine structure branching and angular distributions for photodissociation of S2 (X3Σg–(v = 0), a1Δg and b1Σg+) via the B″3Πu, B3Σu– and 11Πu excited states are reported. In addition, photodissociation of the X3Σg–(v = 0) state of S2 to the second dissociation limit producing S(3P2) + S(1D) is characterized. The present results on S2 photodynamics are compared to those of the well-studied electronically isovalent O2 molecule.

Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers.

A dissociative force field for all-atomistic molecular dynamics calculations has been developed to investigate impact fracture of polymers accompanying dissociation of chemical bonds of polymer main chain. Energy of dimer molecules was evaluated as a function of both bond-length b and bond-angle θ by CASPT2 calculations, whose quality is enough to describe dissociation of chemical bonds. Because we found that the bond dissociation energy D decreases with increasing bond-angle, we employed the Morse-type function VBond (b, θ) = {D - VAngle (θ)}[1 - exp{-α(b - b0 ) - β(b - b0 )2 }] where a quartic function VAngle (θ) = k1 (θ - θ0 ) + k2 (θ - θ0 )2 + k3 (θ - θ0 )3 + k4 (θ - θ0 )4 . This function reproduced well the CASPT2 potential energy surface in a wide range of b and θ. The parameters have been obtained for four popular glassy polymers, polyethylene, poly(methyl methacrylate), poly(styrene), and polycarbonate. © 2019 Wiley Periodicals, Inc.

Importance of Conformational Change in Excited States for Efficient Thermally Activated Delayed Fluorescence

Novel donor–acceptor (D–A) type (monomer) and twin D–A type (dimer) molecules with pretwisted geometrical conformations have been synthesized to investigate the molecular conformation-dependent mec...

Risk HLA class II alleles and amino acid residues in myeloperoxidase–ANCA-associated vasculitis

A genome-wide association study (GWAS) indicated that myeloperoxidase-ANCA associated vasculitis (AAV) is associated with HLA-DQ. However, susceptibility alleles in these loci have been under-investigated. Here we genotyped 258 Chinese patients with myeloperoxidase-AAV and 597 healthy control individuals at HLA DRB1, DQA1, DQB1 and DPB1, and extracted the encoded amino acid sequences from the IMGT/HLA database. The replication cohort included 97 cases and 107 controls. T cell epitopes of myeloperoxidase were predicted and docked to the HLA molecules. We found DQA1∗0302 (odds ratio 2.34 (95% confidence interval 1.75-3.14)) and DQB1∗0303 (odds ratio 1.89 (1.45-2.48)) were risk alleles for myeloperoxidase-AAV. They are in overt linkage disequilibrium (r2 0.69) and the haplotype DQA1∗0302-DQB1∗0303 presents a significant risk (haplotype score 6.39) as well. Aspartate160 on the DQ α chain (odds ratio 2.06 (1.60-2.67)), encoded by DQA1∗0302, and isoleucine185 on the DQ β chain (odds ratio 1.73 (1.38-2.18)), encoded by DQB1∗0303, both located in the α2β2 domains, conferred significant risk for myeloperoxidase-AAV. Homologous modeling showed that DQα∗160D may confer susceptibility to myeloperoxidase-AAV by altering dimerization of the HLA molecules. Thus, more attention should be paid to the roles of amino acids in the α2β2 domains in addition to the α1β1 binding groove of HLA class II molecules.

Structural Basis and Mechanism for Vindoline Dimers Interacting with α,β-Tubulin.

Vinblastine and its derivatives used in clinics as antitumor drugs often cause drug resistance and some serious side effects; thus, it is necessary to study new vinblastine analogues with strong anticancer cytotoxicity and low toxicity. We designed a dimer molecule using two vindoline-bonded dimer vindoline (DVB) and studied its interaction with α,β-tubulin through the double-sided adhesive mechanism to explore its anticancer cytotoxicity. In our work, DVB was docked into the interface between α-tubulin and β-tubulin to construct a complex protein structure, and then it was simulated for 100 ns using the molecular dynamics technology to become a stable and refined complex protein structure. Based on such a refined structure, the quantum chemistry at the level of the MP2/6-31G(d,p) method was used to calculate the binding energies for DVB interacting with respective residues. By the obtained binding energies, the active site residues for interaction with DVB were found. Up to 20 active sites of residues within α,β-tubulin interacting with DVB are labeled in β-Asp179, β-Glu207, β-Tyr210, β-Asp211, β-Phe214, β-Pro222, β-Tyr224, and β-Leu227 and α-Asn249, α-Arg308, α-Lys326, α-Asn329, α-Ala333, α-Thr334, α-Lys336, α-Lys338, α-Arg339, α-Ser340, α-Thr349, and α-Phe351. The total binding energy between DVB and α,β-tubulin is about −251.0 kJ·mol–1. The sampling average force potential (PMF) method was further used to study the dissociation free energy (ΔG) along the separation trajectory of α,β-tubulin under the presence of DVB based on the refined structure of DVB with α,β-tubulin. Because of the presence of DVB within the interface between α- and β-tubulin, ΔG is 252.3 kJ·mol–1. In contrast to the absence of DVB, the separation of pure β-tubulin needs a free energy of 196.9 kJ·mol–1. The data show that the presence of DVB adds more 55.4 kJ·mol–1 of ΔG to hinder the normal separation of α,β-tubulin. Compared to vinblastine existing, the free energy required for the separation of α,β-tubulin is 220.5 kJ·mol–1. Vinblastine and DVB can both be considered through the same double-sided adhesive mechanism to give anticancer cytotoxicity. Because of the presence of DVB, a larger free energy is needed for the separation of α,β-tubulin, which suggests that DVB should have stronger anticancer cytotoxicity than vinblastine and shows that DVB has a broad application prospect.

Synthesis and crystal structure of bis(morpholino dithiocarbamato) Cd(II) complex and its use as precursor for CdS quantum dots using different capping agents

ABSTRACTCadmium(II) morpholine dithiocarbamate complex [Cd(morphdtc)2] was synthesized and characterized by single crystal X-ray crystallography. The molecular structure of the complex showed Cd(II) ion in a distorted 4 + 2 octahedral geometry, in which the two morpholine dithiocarbamates act as bidentate chelating and the central Cd ion bond the sulfur atoms of adjacent morpholine acting as bridging ligands to form centrosymmetric five coordinate dimeric molecules. The Cd(II) complex was thermolysed at 180°C to prepare CdS nanoparticles using three different capping agents. The pXRD patterns revealed a mixture of hexagonal and cubic crystalline phases of CdS nanocrystals. TEM images revealed semi-spherical and spherical nanoparticles, with the size range of 4.50–5.70 nm for OLM-CdS, 3.33–5.96 nm for HDA-CdS, and 3.00–5.83 nm for ODA-CdS. The particle size distribution of the CdS nanocrystallite is within the range 1.06 nm (SD ± 0.73) for OLM-CdS, 0.68 nm, (SD ±0.73) for HDA-CdS and 1.18 nm, (SD ± 0.60) for ODA-CdS. The lattice fringes showed that the particles are almost in the same environment with the interplanar of 0.32 nm for OLM-CdS, 0.34 nm for HDA-CdS, and 0.32 nm ODA-CdS. The band gaps energy were confirmed to be 1.59 eV for OLM-CdS, 1.65 eV for HDA-CdS, and 1.62 eV for ODA-CdS nanoparticles, respectively.

Structure determination of the tetracene dimer in helium nanodroplets using femtosecond strong-field ionization.

Dimers of tetracene molecules are formed inside helium nanodroplets and identified through covariance analysis of the emission directions of kinetic tetracene cations stemming from femtosecond laser-induced Coulomb explosion. Next, the dimers are aligned in either one or three dimensions under field-free conditions by a nonresonant, moderately intense laser pulse. The experimental angular covariance maps of the tetracene ions are compared to calculated covariance maps for seven different dimer conformations and found to be consistent with four of these. Additional measurements of the alignment-dependent strong-field ionization yield of the dimer narrow the possible conformations down to either a slipped-parallel or parallel-slightly rotated structure. According to our quantum chemistry calculations, these are the two most stable gas-phase conformations of the dimer and one of them is favorable for singlet fission.

Resolving the Unpaired-Electron Orbital Distribution in a Stable Organic Radical by Kondo Resonance Mapping.

The adsorption geometry and the electronic structure of a Blatter radical derivative on a gold surface were investigated by a combination of high-resolution noncontact atomic force microscopy and scanning tunneling microscopy. While the hybridization with the substrate hinders direct access to the molecular states, we show that the unpaired-electron orbital can be probed with Ångström resolution by mapping the spatial distribution of the Kondo resonance. The Blatter derivative features a peculiar delocalization of the unpaired-electron orbital over some but not all moieties of the molecule, such that the Kondo signature can be related to the spatial fingerprint of the orbital. We observe a direct correspondence between these two quantities, including a pronounced nodal plane structure. Finally, we demonstrate that the spatial signature of the Kondo resonance also persists upon noncovalent dimerization of molecules.

Modeling Barrier Properties of Intestinal Mucus Reinforced with IgG and Secretory IgA against Motile Bacteria.

The gastrointestinal (GI) tract is lined with a layer of viscoelastic mucus gel, characterized by a dense network of entangled and cross-linked mucins together with an abundance of antibodies (Ab). Secretory IgA (sIgA), the predominant Ab isotype in the GI tract, is a dimeric molecule with 4 antigen-binding domains capable of inducing efficient clumping of bacteria, or agglutination. IgG, another common Ab at mucosal surfaces, can cross-link individual viruses to the mucin mesh through multiple weak bonds between IgG-Fc and mucins, a process termed muco-trapping. Relative contributions by agglutination versus muco-trapping in blocking permeation of motile bacteria through mucus remain poorly understood. Here, we developed a mathematical model that takes into account physiologically relevant spatial dimensions and time scales, binding and unbinding rates between Ab and bacteria as well as between Ab and mucins, the diffusivities of Ab, and run-tumble motion of active bacteria. Our model predicts both sIgA and IgG can accumulate on the surface of individual bacteria at sufficient quantities and rates to enable trapping individual bacteria in mucins before they penetrate the mucus layer. Furthermore, our model predicts that agglutination only modestly improves the ability for antibodies to block bacteria permeation through mucus. These results suggest that while sIgA is the most potent Ab isotype overall at stopping bacterial penetration, IgG may represent a practical alternative for mucosal prophylaxis and therapy. Our work improves the mechanistic understanding of Ab-enhanced barrier properties of mucus and highlights the ability for muco-trapping Ab to protect against motile pathogens at mucosal surfaces.

Immunoglobulin G structure and rheumatoid factor epitopes.

Antibodies are important for immunity and exist in several classes (IgM, IgD, IgA, IgG, IgE). They are composed of symmetric dimeric molecules with two antigen binding regions (Fab) and a constant part (Fc), usually depicted as Y-shaped molecules. Rheumatoid factors found in patients with rheumatoid arthritis are autoantibodies binding to IgG and paradoxically appear to circulate in blood alongside with their antigen (IgG) without reacting with it. Here, it is shown that rheumatoid factors do not react with native IgG in solution, and that their epitopes only become accessible upon certain physico-chemical treatments (e.g. heat treatment at 57 °C), by physical adsorption on a hydrophobic surface or by antigen binding. Moreover, chemical cross-linking in combination with mass spectrometry showed that the native state of IgG is a compact (closed) form and that the Fab parts of IgG shield the Fc region and thereby control access of rheumatoid factors and presumably also some effector functions. It can be inferred that antibody binding to pathogen surfaces induces a conformational change, which exposes the Fc part with its effector sites and rheumatoid factor epitopes. This has strong implications for understanding antibody structure and physiology and necessitates a conceptual reformulation of IgG models.

Dynamics of three-particle fragmentation of (CO2)23+ ions produced by intense femtosecond laser fields

In a momentum coincidence measurement experiment, we studied the three-body fragmentation dynamics of carbon dioxide dimers in intense femtosecond laser fields. The three-dimensional momentum vectors and kinetic energies of the fragments were recorded in a cold-target recoil-ion momentum spectrometer. An analysis shows that ${({\mathrm{CO}}_{2})}_{2}{}^{3+}$ breaks up into ${\mathrm{CO}}_{2}{}^{+}+{\mathrm{CO}}^{+}+{\mathrm{O}}^{+}$ ions through both concerted and sequential fragmentation channels. These two fragmentation channels are consistent with the instantaneous and metastable dissociation channels in the dissociation dynamics of ${\mathrm{CO}}_{2}{}^{2+}$ ion breakup into ${\mathrm{CO}}^{+}$ and ${\mathrm{O}}^{+}$ ions. From Coulomb explosion imaging, our results show that, for the parallel sliding structure of the carbon dioxide dimer molecules, the angle between the C=O bond and the van der Waals bond is $48{}^{\ensuremath{\circ}}$, and the intermolecular nuclear distance $R({\mathrm{CO}}_{2}\text{\ensuremath{-}}{\mathrm{CO}}_{2})$ is 4.0 \AA{}. By tracing the direction of the fragmentation ions, the ${\mathrm{O}}^{+}$ was found to be produced from the C=O bond that is closer to the center of the C-C bond during direct dissociation. These results indicate that the dynamic characteristics of the monomer is retained and gives rise to new dynamics in the molecular cluster complexes. Finally, we have measured angular distributions of ion fragments produced by different dissociation channels of ${({\mathrm{CO}}_{2})}_{2}$, and the results reveal that the structure of the dimer and its relative orientation in the laser field govern the ionization dynamics.

Tunable strong plasmon-exciton coupling between single silver nanocube dimer and J-aggregates

In this paper, single silver nanocube dimer with nanometer-sized gap is designed and numerically simulated. We demonstrate that the electric fields can be highly confined in the gap of nanocube dimer, leading to ultrasmall mode volume of ≈2 × 10-7 μm3. Furthermore, the strong plasmon-exciton coupling in single nanocube dimer coupled with J-aggregate molecules is investigated using coupled oscillator model and we show that the strong plasmon-exciton coupling can be tuned by changing the background refractive index and the concentration of J-aggregate molecules. The tuning of dual strong plasmon-exciton couplings between single rounded silver nanocube dimer and J-aggregate molecules is also investigated, and dual strong couplings can be achieved closely approaching the quantum optics limit benefiting from the ultrasmall mode volume of the proposed system. The proposed systems can be easily prepared and have high experimental feasibility, which has potential applications in integrated nanophotonics such as sensing and all-optical switches.

Bicolor switching mechanism of multifunctional light-emitting molecular material in solid phase

Abstract Multifunctional light-emitting molecular materials have attracted great attention recently, while the amounts are still quite limited. The Cz-AQ molecule with thermally activated delayed fluorescence, aggregation-induced emission and mechanochromic luminescence properties was reported and the bicolor electroluminescence was found in film recently by Jiang's group (J. Mater. Chem. C 5 (2017) 12031–12034). In this paper, the bicolor switching mechanism of the Cz-AQ molecule in solid phase is studied based on first-principles and combined quantum mechanics and molecular mechanics calculations. Our results indicate that the emission of Cz-AQ in solid phase does not come from monomers but dimers. The emission colors have close relationship with intermolecular positions of two molecules in dimers. There is no need of conversion of lattice types for color switching, and slight variation of relative position of molecules in dimers will induce the emission color change between red and yellow. Our theoretical study not only gives reasonable explanation of experimental results but also provides some insights on the design of new type multifunctional light-emitting molecules.

The clean and mild synthesis, crystal structure, and intra-molecular hydrogen bond study of substituted new 4,8-dihydropyrano[3,2-b]-pyrans containing chlorokojic acid moiety

A safe, green and convenient process was developed for the synthesis of a novel group of 4,8-dihydropyrano[3,2-b]-pyrans by dialkyl acetylenedicarboxylates and alkyl isocyanides being trapped by chlorokojic acid in good to excellent yields at ambient temperature. Characterization of all structures was carried out by FT-IR and 1H and 13C NMR spectrometers, and two compounds were analyzed using X-ray diffraction technique. Crystal structures showed an intramolecular hydrogen bond and stacking of the dimeric (RS) molecules with the unit cell along the a-axis.