Single Molecular Structure Research Articles

Laser-induced electron diffraction: Imaging of a single gas-phase molecular structure with one of its own electrons.

Among the many methods to image molecular structure, laser-induced electron diffraction (LIED) can image a single gas-phase molecule by locating all of a molecule's atoms in space and time. The method is based on attosecond electron recollision driven by a laser field and can reach attosecond temporal resolution. Implementation with a mid-IR laser and cold-target recoil ion-momentum spectroscopy, single molecules are measured with picometer resolution due to the keV electron impact energy without ensemble averaging or the need for molecular orientation. Nowadays, the method has evolved to detect single complex and chiral molecular structures in 3D. The review will touch on the various methods to discuss the implementations of LIED toward single-molecule imaging and complement the discussions with noteworthy experimental findings in the field.

Molecular symmetry change of perfluoro-n-alkanes in ‘Phase I’ monitored by infrared spectroscopy

Phase diagram of polytetrafluoroethylene (PTFE) comprises four regions. Phases II and IV are characterized by twisted perfluoroalkyl (Rf) chains having different twisting rate of 13/6 and 15/7, respectively, while Phase III is characterized by a planer trans-zigzag molecular skeleton like a normal alkyl chain. These are confirmed by X-ray and electron diffraction and have already been established. Unlike these, Phase I is left an unresolved matter. This phase is complicated indeed and is not symbolized by a single molecular structure. At an ambient pressure, Phase I is the temperature region above 30 ºC (303 K), and the helical molecular structure is supposed to be gradually untwisted with an elevating temperature. This untwisting image is roughly suggested by the diffraction, neutron scattering, and thermal expansion techniques, but the conventional approaches have all experimental limitations because the untwisting accompanies disorder (or defect) in the twist along the chain. To explore the transition between two different helical structures of the Rf chain having disordered structures, vibrational spectroscopic techniques are expected to be an alternative approach. For infrared spectroscopy, for example, the twisting rate of the molecule is simply recognized as a degree of molecular symmetry. Here, we show that the band progression peaks of the CF2 symmetric stretching vibration mode are quite sensitive and useful for pursuing the molecular symmetry change in Phase I for both peak intensity and position using perfluoro-n-alkanes having different chain length covering both even and odd number of the CF2 groups.Graphical abstract

Predicting equilibrium distributions for molecular systems with deep learning

Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure but rather determined from the equilibrium distribution of structures. Conventional methods for obtaining these distributions, such as molecular dynamics simulation, are computationally expensive and often intractable. Here we introduce a deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems. Inspired by the annealing process in thermodynamics, DiG uses deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system such as a chemical graph or a protein sequence. This framework enables the efficient generation of diverse conformations and provides estimations of state densities, orders of magnitude faster than conventional methods. We demonstrate applications of DiG on several molecular tasks, including protein conformation sampling, ligand structure sampling, catalyst–adsorbate sampling and property-guided structure generation. DiG presents a substantial advancement in methodology for statistically understanding molecular systems, opening up new research opportunities in the molecular sciences.

Energy-transfer-induced [3+2] cycloadditions of N-N pyridinium ylides.

Photocycloaddition is a powerful reaction to enable the conversion of alkenes into high-value synthetic materials that are normally difficult to obtain under thermal conditions. Lactams and pyridines, both prominent in pharmaceutical applications, currently lack effective synthetic strategies to combine them within a single molecular structure. Here we describe an efficient approach to diastereoselective pyridyl lactamization via a photoinduced [3+2] cycloaddition, based on the unique triplet-state reactivity of N-N pyridinium ylides in the presence of a photosensitizer. The corresponding triplet diradical intermediates allow the stepwise radical [3+2] cycloaddition with a broad range of activated and unactivated alkenes under mild conditions. This method exhibits excellent efficiency, diastereoselectivity and functional group tolerance, providing a useful synthon for ortho-pyridyl γ- and δ-lactam scaffolds with syn-configuration in a single step. Combined experimental and computational studies reveal that the energy transfer process leads to a triplet-state diradical of N-N pyridinium ylides, which promotes the stepwise cycloaddition.

Ultra-fast semi-empirical quantum chemistry for high-throughput computational campaigns with Sparrow.

Semi-empirical quantum chemical approaches are known to compromise accuracy for the feasibility of calculations on huge molecules. However, the need for ultrafast calculations in interactive quantum mechanical studies, high-throughput virtual screening, and data-driven machine learning has shifted the emphasis toward calculation runtimes recently. This comes with new constraints for the software implementation as many fast calculations would suffer from a large overhead of the manual setup and other procedures that are comparatively fast when studying a single molecular structure, but which become prohibitively slow for high-throughput demands. In this work, we discuss the effect of various well-established semi-empirical approximations on calculation speed and relate this to data transfer rates from the raw-data source computer to the results of the visualization front end. For the former, we consider desktop computers, local high performance computing, and remote cloud services in order to elucidate the effect on interactive calculations, for web and cloud interfaces in local applications, and in world-wide interactive virtual sessions. The models discussed in this work have been implemented into our open-source software SCINE Sparrow.

Hybrid Molecules as Potential Drugs for the Treatment of HIV: Design and Applications.

Human immunodeficiency virus (HIV) infection is a major problem for humanity because HIV is constantly changing and developing resistance to current drugs. This necessitates the development of new anti-HIV drugs that take new approaches to combat an ever-evolving virus. One of the promising alternatives to combination antiretroviral therapy (cART) is the molecular hybrid strategy, in which two or more pharmacophore units of bioactive scaffolds are combined into a single molecular structure. These hybrid structures have the potential to have higher efficacy and lower toxicity than their parent molecules. Given the potential advantages of the hybrid molecular approach, the development and synthesis of these compounds are of great importance in anti-HIV drug discovery. This review focuses on the recent development of hybrid compounds targeting integrase (IN), reverse transcriptase (RT), and protease (PR) proteins and provides a brief description of their chemical structures, structure–activity relationship, and binding mode.

Physicochemical Characteristics and Antidiabetic Properties of the Polysaccharides from Pseudostellaria heterophylla.

This study aimed to investigate the Pseudostellaria heterophylla polysaccharides (PF40) physicochemical and antidiabetic characteristics. The ultraviolet–visible (UV) spectra, Fourier transform infrared radiation (FT-IR) spectra, nuclear magnetic resonance (NMR) spectra, zeta potential, surface characteristics, and conformational and thermal stability properties of PF40 were characterized. X-ray diffraction (XRD) and scanning electron microscopy (SEM), combined with Congo red test, revealed that PF40 powder has mainly existed in amorphous form with triple-helix conformation. The single-molecular structure of PF40 exhibited a multi-branched structure extending from the center to the periphery by scanning probe microscopy (SPM) scanning. The monosaccharide residue of PF40 was an α-pyranoid ring and exhibits good stability below 168 °C. Experimental studies on antidiabetic characteristics found that PF40 could significantly improve STZ-induced intestinal mucosal damage and reduce the apoptosis of villus epithelial cells. PF40 combined with metformin could significantly improve the symptoms of insulin resistance in type 2 diabetes mellitus (T2DM) rats, the molecular mechanism might be through inhibiting the expression of RORγ protein and increasing Foxp3 protein in the jejunum of T2DM rats, and then restoring the STZ-induced imbalance of T helper 17(Th17)/ regulatory T cells (Treg) cells, thereby maintaining intestinal immune homeostasis. Results identified in this study provided important information regarding the structure and antidiabetic characteristics of Pseudostellaria heterophylla polysaccharides, which can contribute to the development of Pseudostellaria heterophylla polysaccharides for industrial purposes in the future.

Effect of the nuclearity on the catalytic performance of a series of Pd(II) complexes in the Suzuki-Miyaura reaction

Development of well-defined multivalent systems with densely packed multiple functional groups located within a single molecular structure provides an excellent opportunity to generate catalysts of enhanced activity. A series of mono-, di- and trinuclear Pd(II) complexes based on polyketonate ligands allied with 2,2′-bipyridine has been designed, synthesized and fully characterized in both solution and solid state. The mono-, di- and tritopic β-diketonate molecules serve as scaffolds for Pd(II) active sites which, in the two latter cases, are forced into close proximity. Application of the complexes as catalysts in Suzuki-Miyaura cross-coupling as a model reaction has revealed significant differences in reaction yields and a trend in reactivity reflecting their nuclearity.

A Review of the Recent Developments of Molecular Hybrids Targeting Tubulin Polymerization.

Microtubules are cylindrical protein polymers formed from αβ-tubulin heterodimers in the cytoplasm of eukaryotic cells. Microtubule disturbance may cause cell cycle arrest in the G2/M phase, and anomalous mitotic spindles will form. Microtubules are an important target for cancer drug action because of their critical role in mitosis. Several microtubule-targeting agents with vast therapeutic advantages have been developed, but they often lead to multidrug resistance and adverse side effects. Thus, single-target therapy has drawbacks in the effective control of tubulin polymerization. Molecular hybridization, based on the amalgamation of two or more pharmacophores of bioactive conjugates to engender a single molecular structure with enhanced pharmacokinetics and biological activity, compared to their parent molecules, has recently become a promising approach in drug development. The practical application of combined active scaffolds targeting tubulin polymerization inhibitors has been corroborated in the past few years. Meanwhile, different designs and syntheses of novel anti-tubulin hybrids have been broadly studied, illustrated, and detailed in the literature. This review describes various molecular hybrids with their reported structural–activity relationships (SARs) where it is possible in an effort to generate efficacious tubulin polymerization inhibitors. The aim is to create a platform on which new active scaffolds can be modeled for improved tubulin polymerization inhibitory potency and hence, the development of new therapeutic agents against cancer.

A robust dual-channel fluorescence-enhanced probe for duplex imaging of endogenous HClO/ClO- in living cells and in zebrafish

A unique fluorescent probe, MCB, for HClO/ClO- was rationally constructed by integrating methylene blue, 7-hydroxycoumarin, and two HClO-specific reacting moieties into a single molecular structure. Distinct from other published cases, MCB displayed remarkable dual-channel fluorescence enhancement, peaked at 464 and 700 nm respectively, which simultaneously provided two crosstalk-free fluorescence channels, blue and NIR channels, for mutual corroboration, and hence improving the reliability of the detection results. More importantly, MCB exhibited excellent sensing properties for HClO/ClO-, such as fast response (within 90 s), high sensitivity (LOD as low as 3.9 nM based on blue fluorescence channel), and sufficient selectivity. Significantly, MCB was successfully utilized for dual-channel imaging of HClO/ClO-in living cells and zebrafish, thereby holding the potential for research that focused on elucidating the biological roles of HClO/ClO-.

Surface discharge of bulk materials investigated from change of charge trap characteristics of polyimide single molecular chain

Surface discharge is one of the reasons for insulation failure. Polyimide (PI) is used in gas-solid insulation of high-frequency electric power equipment. Therefore, based on density functional theory, the effects of single molecular chain structure, energy level, density of states, electrostatic potential, excited state and other micro parameters under external electric field on trap formation and surface discharge of both PI and polar- group- OH<sup>– </sup>affected PI are discussed from the atomic and molecular level. The results show that the structure of PI is crimped and the dipole moment increases under external electric field, which is easy to accumulate charges to form space charge center, especially after the introduction of polar group OH<sup>–</sup>. In the PI molecules, hole traps are formed in the benzene ring region, and electron traps are formed in the imide ring region. The number of electron trap energy levels is large, in which the space charge trap depth gradually deepens with the increase of external electric field. After the introduction of polar group OH<sup>–</sup>, the excitation energy of PI molecules decreases, which makes the electrons inside the molecules excited easily. The spatial separation of electrons and holes decreases with the increase of electric field, which is conducive to the recombination of holes and electrons to emit photons.

Micro Nanoengraving Technology and Aesthetic Practice of Architectural Sculpture Art

Micro nanotechnology refers to the emerging technology of material production using a single atomic or molecular structure. The structure and size of materials range from one to 100 microns or nanometers. In this paper, micro nanotechnology is used to study the aesthetic practice of sculpture technology and architectural sculpture art. This paper aims to combine traditional art ideas with science and technology to promote common development. This paper first introduces the micro nanoengraving technology and architectural sculpture art, it includes the definition of works, classification of works, and research on artistic commonalities and differences, and then summarizes the characteristics of micro nanoengraving materials. Finally, this paper will carry out aesthetic practice of sculpture works based on micro nanocreation. Finally, this paper compares with the works created by traditional technology. The results show that the recognition and creativity evaluation of sculpture works based on micro nanocreation have reached more than 8 points. It verifies the effectiveness of the technology.

Regulation mechanism of ultrasonication on surface hydrophobicity of scheelite

Centering on the roles of ultrasound in flotation kinetics, adsorptions of sodium oleate and scheelite, heat of adsorption and mineral surface properties, we investigated the effects of ultrasonic pre-treatment on scheelite surface dissolution, as well as properties and microstructure of sodium oleate solution. As a result, the ultrasonic treatment of sodium oleate or scheelite promoted the adsorption of sodium oleate on the surface of scheelite, which improved adsorption heat, thermal reaction rate, surface hydrophobicity, flotation rate and recovery rate of scheelite. However, the ultrasonic treatment effect of sodium oleate was better than that of scheelite. The dissociation of sodium oleate molecules was promoted by the ultrasound reduces the surface tension of collector solution to enhance its solution activity. In the meantime, the agglomeration structures of sodium oleate were disrupted by ultrasonication to form a small or single molecular structure, which helped accelerate the solute migration speed and reduced induction time between sodium oleate and scheelite. Ultrasonic treatment removed the adhesion of fine particles on the surface of scheelite and the severely corroded mineral surface, which accelerated the dissolution and increased the number of Ca 2+ reactive sites. • The ultrasound increases the hydrophobicity of surface. • The ultrasound improves the flotation rate and recovery rate. • The ultrasound alters the properties and microstructure of NaOL. • The ultrasound decreases the adhesion power between NaOL and scheelite. • The ultrasound adjusts the ratio of Ca/W on the surface of scheelite.

Exploring molecular structure characteristics and chemical index of Qinghua bituminous coal: A comprehensive insight from single molecule of macerals to particles with various sizes

Understanding the relationship between the coal structure and its reactive behaviour is of great significance to achieve clean coal conversion and its efficient utilisation. One of the key tasks is to elucidate the molecular structure and chemical bonding information of coal. Owing to the complexity of the chemical structure of coal, studies on the molecular structure of coal, especially coal models with complex particle structures of different sizes for bituminous coal from northwest China, are highly warranted. In this work, the molecular structure characteristics and chemical index of a Qinghua bituminous coal sample collected from the Ningdong area, China, were assessed. Using a combination of material characterization, computation, and molecular modelling methods, a standard method for modelling complex coal structures from single molecules of macerals to particles of various sizes was developed. The single molecular structure of vitrinite and inertinite present in Qinghua coal can be expressed as C269H196N4O13S and C255H179N3O14S, respectively. Then, a series of complex particle models of various sizes were established based on the single molecular structure models of vitrinite and inertinite. Among these models, the size of the complex particles was as large as 11 nm, with the total atomic number approaching 60,000. Furthermore, the energetic and structural features of the complex coal particle structures were also explored based on their energy decomposition and radial distribution function analysis. In addition, the chemical structure index analysis was performed for different coal macerals to further understand the internal relationship between its structure and application.

Construction of molecular structure model of Tunlan coal and its microscopic physicochemical mechanism

Physicochemical structure is essential for understanding physiochemical properties of coal reservoir and coalbed methane (CBM) occurrence. In this work, ultimate analysis, 13C nuclear magnetic resonance spectra (NMR), Fourier transform infrared spectroscopy (FTIR) and gas chromatograph/mass spectrometer (GC/MS) tests were adopt to investigate the coal molecular structure information. Then, by means of molecular simulation, stable three-dimensional (3D) molecular structure and physicochemical structure models of Tunlan coal were established to reveal the physicochemical response at a molecular level. Results show that compared with the single molecular structure, angle and torsion energies in nanopore structure play a more important role in maintaining a stable and stereoscopic structure. While the electrostatic energy in non-bond energy can simulate to form nanopore space in coal. Then, with the dissolution of low molecular weight compounds (LMWCs), the pore volume (PV) of micropores increases gradually, while the corresponding specific surface area (SSA) decreases first and then increases, suggesting that pore expansion and pore increase effects are dominant in the early and the later dissolution stages, respectively. Furthermore, observing physicochemical response, total pore structure distribution depends on whether vertical or horizontal changes of basic structure units in coal make a great contribution in this evolution stage. Actually, when the aromatic layer is mainly the increase of the stacking height Lc, it is easy to result in the decrease of total SSA and PV. In contrast, for mainly the increase of the diameter La, all pores in coal present an increase characteristic to induce the increase of total SSA and PV.

OsDREB2A Gene Polymorphism Does Not Affect Salinity Tolerance Potency of Local Rice Varieties from Banten

Indonesia possesses vast coastal agricultural land areas with high salinity. This high salinity is a threat to rice productivity which may decrease to 79.8%. Banten province of Indonesia houses many local rice varieties which have salinity tolerance potency based on its agronomical characters. The adaptability of rice plant in high salinity soil can be affected by OsDREB2A gene, which encodes transcription factors from several salt-tolerant signaling pathway genes. The aims of this study were to find out the possible polymorphism of OsDREB2A gene from Banten local rice varieties. The polymorphism of OsDREB2A analyzed by Single Nucleotide Polymorphism (SNP) and possible molecular structure. OsDREB2A gene was amplified using DNA from Tambleng, Bulu Putih, and Pare Caok varieties as templates through PCR method with a pair of specific primers. DNA fragments obtained were analyzed by means of series of analysis software. From those analysis we obtained 840 bp, 836 bp, and 850 bp gene fragments from Tambleng, Bulu Putih, and Pare Caok varieties, respectively. There is polymorphism of OsDREB2A due to some mutation yet does not massively alter its protein structure. From this study, we suggest that Tambleng, Bulu Putih, and Pare Caok varieties potential for salinity stress resistance genetically.

Effect of shock waves on enhancing the optical properties of Ammonium Pentaborate Hexahydrate single crystal molecular structure

Ammonium Pentaborate Hexahydrate (APBHH), a novel inorganic nonlinear optical single crystal was grown by slow evaporation solution growth method and the Properties of the grown crystals were investigated. The grown crystal was subjected to single crystal XRD and Powder X-ray diffraction analysis to confirm the crystal structure to the monoclinic system with centrosymmetric nature. The presence of various functional groups has been identified by using FT-IR spectral analysis ranging between 4000 and 500 cm−1. The percentage of optical absorbance was ascertained by recording the UV-Vis spectrum, crystals shows transparent in the entire visible region with a 5.56 eV optical bandgap. The dielectric constant and dielectric loss of APBHH crystal as a function of frequency and an AC resistivity, conductivity with impedance also were calculated at room temperature. Ammonium Pentaborate Hexahydrate (APBHH) crystal under pre and post shock loaded conditions. A shock wave of Mach number 1.7 was utilized for the present investigation which was generated by a table-top pressure driven shock tube. The optical properties of test material are investigated by UV-Visible spectrometer over the range between 200 and 800 nm. The observed result showed that the transparency of the crystal increase by applying Shock Waves.

Helicate Lanthanide Complexes: The Luminescent Elements

Luminescent lanthanide (Ln) complexes based on chelate effects will be introduced using a series of hexadentate bipyridine derivatives as their ligand moieties. The molecules form a single helicate molecular structure with a Ln-coordination. Molecular distortion and various derivations induce the intended luminescence and characteristic molecular conformation, which depend on atmosphere or media. It would be a supportive case to design novel units of Ln components for emission.

Optimization analysis of polyurethane based mixed matrix gas separation membranes by incorporation of gamma-cyclodextrin metal organic frame work

In this article, a polyurethane-based mixed matrix membrane employed for the separation of carbon dioxide from methane (CO2/CH4) and permeability as well as selectivities of both the gases were determined. Gamma-cyclodextrin metal–organic framework (γ-CD-MOF) was used as a filler and incorporated (0.2–1 wt%) weight percentage into the polyurethane matrix for the fabrication of dense gas separation membrane through the solution casting method. These membrane samples were undergone following characterization techniques, i.e., FTIR, SEM, XRD and UTS for qualitative analysis. Gamma-CD-MOF equipped with an ideal cavity of 17 A diameter and an abundance of the hydroxyl group in a single molecular structure. This unique characteristic stands out Gamma-CD-MOF as the most preferential filler that can adsorb carbon dioxide from mixture of gases. Membrane samples were tested using single and mixed gases and results reflected the enhancement in carbon dioxide (CO2) permeability. The best CO2/CH4 selectivity of 28.56 is achieved by PU/γ-CD-MOF 0.2 wt%.

Vibrational spectra of pyrazinamide and isoniazid studied by terahertz spectroscopy and density functional theory.

Pyrazinamide and isoniazid, as two first-line anti-tuberculosis drugs, are investigated by terahertz time-domain spectroscopy (THz-TDS). Both pyrazinamide and isoniazid have three absorption peaks, at 0.50, 0.71, 1.42THz and 1.16, 1.46, 1.56THz, respectively, which can be used as the basis for qualitative identification of these two drugs. In order to gain insight into the origin of the characteristic absorption peaks, density functional theory (DFT) based on single molecular, dimer, and crystalline structures of pyrazinamide and isoniazid are performed. The purpose of the calculation based on the single molecular structure is to understand the intramolecular interaction, while those based on the dimer and crystalline structures are to investigate the intermolecular interactions in PNZ and INZ. Comparing the theoretical results of the dimer and crystalline based structures reveals that the crystalline structure leads to vibrational spectra that are closer to the experimental values in terms of the number of absorption peaks and the positions of the absorption peaks. Vibrational mode assignments can be summarized as that the characteristic absorption peaks of pyrazinamide mainly come from intermolecular interaction, and the characteristic absorption peaks of isoniazid originate from both the intramolecular and intermolecular interactions. Our experimental and theoretical results indicate that the combination of THz-TDS with DFT is an effective approach for identification of molecules with pharmaceutical significance.