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The three possible 1-(n-pyridinyl)butane-1,3-diones (nPM) have been synthesized. Structures, tautomerism, and conformations are investigated by means of DFT calculations. 1H and 13C NMR spectra are assigned, and deuterium isotope effects on 13C chemical shifts have been measured. Analysis of the isotope effects leads to the equilibrium constants of the keto–enol tautomers. Some interesting differences are seen between the three compounds and the phenyl analogs. The isotope effects can also rank the hydrogen bonds of the compounds, with the one with nitrogen in the three positions of the pyridine ring as the weakest. Structures, conformers, energies, and NMR nuclear shieldings are calculated using DFT calculations at the B3LYP/6-311++G(d,p) level.

Here, the impact of different groups on the geometrical parameters, dipole moments, atomic charges, stabilization and solvation energies, molecular electrostatic potentials, densities rings, positions IR and UV bands and NMR chemical shifts of all members of the series of 1X-benzotriazole derivatives (X= H, CH3, Cl, NH2and OH) have been investigated by using hybrid B3LYP/6-311++G** calculations because, so far, correlations among their properties neither the vibrational analyses are reported yet. The polarity of N-X bonds, electronegativity, donor/acceptor characteristics of the different X groups were analysed for all members. The polarity of N1-X4 bonds have influence on dipole moments, volumes and on bond lengths of both rings while the chlorinated derivative has a higher reactivity due to its higher global electrophilicity index. NBO and AIM studies reveal the strong influence of Cl on densities of both rings of CBT and, on this derivative. Harmonic force fields evidence very good correlations between stretching force constants and assignments.

Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.

This article focuses on the challenges of hit finding and data reduction in serial crystallography (SX). An effective and reliable Bragg-peak-finding method, called robust peak finder (RPF), has been developed. RPF is based on the principle of robust statistics and can be used for SX data analysis., A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of ‘robust statistics’ has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or ‘vetoing’ of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.

Time-resolved crystallography enabled the visualization of protein molecular motion during reaction. While light is commonly used to initiate reactions in time-resolved crystallography, only a small number of proteins can in fact be activated by light. However, many biological reactions can be triggered by the interaction of proteins with ligands. The sample delivery method presented here uses a mix-and-extrude approach based on 3D printed microchannels in conjunction with a micronozzle to study the dynamics of samples in viscous media that can be triggered by diffusive mixing. The device design allows for mixing of ligands and protein crystals in a time window of 2 to 20 seconds. The device characterization using a model system (fluorescence quenching of iq-mEmerald proteins by copper ions) demonstrated that ligand and protein crystals, each within the lipidic cubic phase, can be mixed efficiently. The potential use of this approach for time-resolved membrane protein crystallography to support in the development of new drugs is also discussed.Synopsis3D printed mixing-HVE devices address time-resolved membrane protein crystallography challenges via compact dual-flow LCP injection.Abstract Figure

In this study, the molecular structure, tautomerization, conformational stability, and electronic energies of 25 enols and keto forms of methyl acetoacetate (MAA) were examined theoretically using DFT and experimentally by IR, Raman, and UV spectroscopy. According to the theoretical and experimental results, three more stable tautomer’s including an enol (2EU1-I) and two ketos (DK1 and DK2) forms in the gas phase, and solutions have been obtained. Using equilibrium ratios in the gas phase and different solvents at various levels of theory, the abundance of enol was determined. Outcomes indicated that the content of cis-enol or keto forms depended on to phase. In gas phase, cis-enol form is as major form. Conventional and unconventional intramolecular hydrogen bonds for cis-enol and keto forms, respectively, were considered via AIM. Also, using NBO in terms of E(2) values, the enol and keto forms, and the hydrogen bond strength interpreted. By recording the vibrational spectra in various polar and non-polar solvents, deuterated analog, deconvolution, and calculating potential energy distribution of cis-enol for MAA, the strong IR bands were obtained at about 1755–1715 cm−1 regions show the existence of two keto forms in the sample. Also, two medium intensity bands at 1654 and 1630 cm−1 were assigned to the chelated ring of cis-enol form. Finally, the UV spectra in different solvents and frontier molecular orbitals were shown that hydrogen bond strength in the enol form of MAA is weaker than AA. Also, the content of keto forms increased in polar solvents.

The interaction between the graphene sheet and adsorbing molecules is investigated as a considerable potential in graphene sensors. The decoration of graphene by chalcogen atoms has improved the CO2 and C2H2 storage capacity via density functional theory calculations, which determine the significant and suitable gas sensor. The distinction of capture and separation of C2H2 from CO2 via absorbents is a great challenge due to the high similarity in kinetic diameters and boiling points, and reactive properties. The obtained results reveal that the C2H2 adsorption energy on the Te-decorated graphene sheet is higher than CO2, which could be corresponded to nonmetal tellurium sensitivity on the modified graphene surface. Additionally, the CO2 adsorption energy on the Te-decorated graphene sheet is the highest in comparison with pristine graphene and Se-decorated graphene. The orbital analysis, such as the density of states as well as frontier molecular orbital, has been studied for indicating the kind of interaction (physisorption or chemisorption). The electron density difference and electron localization function and localized orbital locator analyses assign apparent changes in the distribution of electrons about pristine graphene, Se-decorated graphene, and Te-decorated graphene in the presence of gas molecules adsorption. To the best of our knowledge, this is the first time the quantum chemistry methods are used to find the positive effect of nonmetal (Se, Te) atoms for C2H2 capture. Ultimately, Te-decorated graphene has been detected as the best adsorbent in sensing C2H2 gas.

By non-equilibrium Green's function joined with first-principles density functional theory, the transport behaviour of 4-phenylamino-3-penten-2-one, APO-NPh molecular wire in terms of its enol and ...

Journal of applied crystallography 55, 1549 - 1561 (2022). doi:10.1107/S1600576722009815, X-ray crystallography has witnessed a massive development over the past decade, driven by large increases in the intensity and brightness of X-ray sources and enabled by employing high-frame-rate X-ray detectors. The analysis of large data sets is done via automatic algorithms that are vulnerable to imperfections in the detector and noise inherent with the detection process. By improving the model of the behaviour of the detector, data can be analysed more reliably and data storage costs can be significantly reduced. One major requirement is a software mask that identifies defective pixels in diffraction frames. This paper introduces a methodology and program based upon concepts of machine learning, called robust mask maker (RMM), for the generation of bad-pixel masks for large-area X-ray pixel detectors based on modern robust statistics. It is proposed to discriminate normally behaving pixels from abnormal pixels by analysing routine measurements made with and without X-ray illumination. Analysis software typically uses a Bragg peak finder to detect Bragg peaks and an indexing method to detect crystal lattices among those peaks. Without proper masking of the bad pixels, peak finding methods often confuse the abnormal values of bad pixels in a pattern with true Bragg peaks and flag such patterns as useful regardless, leading to storage of enormous uninformative data sets. Also, it is computationally very expensive for indexing methods to search for crystal lattices among false peaks and the solution may be biased. This paper shows how RMM vastly improves peak finders and prevents them from labelling bad pixels as Bragg peaks, by demonstrating its effectiveness on several serial crystallography data sets., Published by Wiley-Blackwell, [S.l.]

In this research, using nonequilibrium green’s function integrated with density functional theory, we investigate the electronic transport properties of a β-diketone (2,6-dimethyl-3,5-heptanedione) molecular wire induced by hydrogen transfer. The title molecule can be converted between two enol and keto forms. The electronic transmission factors, spatial spreading of molecular projected self-consistent Hamiltonian orbitals, on–off ratio, I–V characteristics, three different adsorption types (hollow, top, and bridge), the alteration of the electrode materials, Y, (Y = Au, Ag, and Pt), and HOMO–LUMO gaps relevant to these forms are thoroughly discussed. It can be concluded that due to the deformation of the title molecule (enol → keto), there is a noticeable change in conductivity. As a result of this deformation, the conductivity is switched from on state (high conductivity and low resistance) to off state (low conductivity and high resistance).

Liquid sample delivery systems are used extensively for serial femtosecond crystallography at X-ray free-electron lasers (XFELs). However, misalignment of the liquid jet and the XFEL beam leads to the X-rays either partially or completely missing the sample, resulting in sample wastage and a loss of experiment time. Implemented here is an algorithm to analyse optical images using machine vision to determine whether there is overlap of the X-ray beam and liquid jet. The long-term goal is to use the output from this algorithm to implement an automated feedback mechanism to maintain constant alignment of the X-ray beam and liquid jet. The key elements of this jet alignment algorithm are discussed and its performance is characterized by comparing the results with a manual analysis of the optical image data. The success rate of the algorithm for correctly identifying hits is quantified via a similarity metric, the Dice coefficient. In total four different nozzle designs were used in this study, yielding an overall Dice coefficient of 0.98.

Density functional theory (DFT) and Atoms-in-Molecules (AIM) analyses as well as Fourier transform Infrared, Raman, and UV spectra have been used to investigate the structure and vibrational spectra of bis(3,5-heptanedionato)copper(II) (Cu(HPD)2). To explore the effect of ethyl substitution with the methyl and t-But groups in the β-position, two different complexes have been chosen, namely, copper (II) acetylacetonate Cu(acac)2 and copper (II) 2,2,6,6-tetramethylheptane-3,5-dionate (Cu(TMHD)2), respectively. The experimental IR and Raman wavenumbers have been fully assigned, using the calculated ones. The calculated and experimental results are in good agreement. The metal–O bond strength was investigated by geometry calculations and spectroscopic results to realize the substitution effect. The metal–ligand bond strength in Cu(HPD)2 is between the corresponding ones in Cu(THMD)2 and Cu(acac)2.

Graphical abstract The synthetic cyclohexenecarboxylate ester antiviral Oseltamivir (O) have been theoretically studied by B3LYP/6–311 + + G** calculations to estimate its reactivity and behaviour in gas and aqueous media. The most stable structure obtained in above media is consistent with that reported experimental for Oseltamivir phosphate. The solvation energy value of (O) in aqueous media is between the predicted for antiviral Idoxuridine and Ribavirin. Besides, (O) containing a NH2 group and NH group reveals lower solvation energy compared with other antiviral agents with an NH2 group, such as Ribavirin, Cidofovir, and Brincidofovir. Atomic charges on N and O atoms in acceptors and donor groups reveal different behaviours in both media, while the natural bond orbital (NBO) studies show a raised stability of (O) in aqueous solution. This latter resulted is in concordance with the lower reactivity evidenced in water. Frontier orbital studies have revealed that (O) in gas phase has a very similar gap value to antiviral Cidofovir used against the ebola disease, while Chloroquine in the two media are more reactive than (O). This study will allow to identify (O) by using vibrational spectroscopy because the 144 vibration modes expected have been assigned using the harmonic force fields calculated from the scaled mechanical force field methodology (SQMFF). Scaled force constants for (O) in the mentioned media are also reported for first time. Due to hydration of the C = O and NH2 groups by solvent molecules, the calculations in solution produce variations not only in the IR wavenumbers bands, but also in their intensities. Supplementary Information The online version contains supplementary material available at 10.1007/s00894-021-04962-3.

In this study, the electronic transport properties of 2-amino-4,5-bis(2,5-dimethylthiophen-3-yl)furan-3-carbonitrile (as a diarylethene) and its 3 derivatives in R position (R = H, –NH2, and –NO2) have been studied by non-equilibrium green’s function joint with density functional theory. This molecule can be converted from closed form to open form by ultraviolet radiation or visible light. Several parameters, including different molecular geometries, the influence of electrode constituents (Pt, Au, and Ag) and adsorption types (bridge, hollow, and top), I–V characteristics, on–off ratio, HOMO–LUMO gaps, and electronic transmission coefficients T(E), have been investigated. The results showed that as the molecule changes from closed form to open form (closed → open), conductivity changes from on state (high conductivity) to off state (low conductivity).

Journal of synchrotron radiation 29(2), 331 - 346 (2022). doi:10.1107/S1600577521013370, The Sample Environment and Characterization (SEC) group of the European X-ray Free-Electron Laser (EuXFEL) develops sample delivery systems for the various scientific instruments, including systems for the injection of liquid samples that enable serial femtosecond X-ray crystallography (SFX) and single-particle imaging (SPI) experiments, among others. For rapid prototyping of various device types and materials, sub-micrometre precision 3D printers are used to address the specific experimental conditions of SFX and SPI by providing a large number of devices with reliable performance. This work presents the current pool of 3D printed liquid sample delivery devices, based on the two-photon polymerization (2PP) technique. These devices encompass gas dynamic virtual nozzles (GDVNs), mixing-GDVNs, high-viscosity extruders (HVEs) and electrospray conical capillary tips (CCTs) with highly reproducible geometric features that are suitable for time-resolved SFX and SPI experiments at XFEL facilities. Liquid sample injection setups and infrastructure on the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument are described, this being the instrument which is designated for biological structure determination at the EuXFEL., Published by Wiley-Blackwell, [S.l.]

Advances in modern interface- and material sciences often rely on the understanding of a system's structure-function relationship. Designing reproducible experiments that yield in situ time-resolved structural information at fast time scales is therefore of great interest, e.g., for better understanding the early stages of self-assembly or other phase transitions. However, it can be challenging to accurately control experimental conditions, especially when samples are only available in small amounts, prone to agglomeration, or if X-ray compatibility is required. We address these challenges by presenting a microfluidic chip for triggering dynamics via rapid diffusive mixing for in situ time-resolved X-ray investigations. This polyimide/Kapton-only-based device can be used to study the structural dynamics and phase transitions of a wide range of colloidal and soft matter samples down to millisecond time scales. The novel multiangle laser ablation three-dimensional (3D) microstructuring approach combines, for the first time, the highly desirable characteristics of Kapton (high X-ray stability with low background, organic solvent compatibility) with a 3D flow-focusing geometry that minimizes mixing dispersion and wall agglomeration. As a model system, to demonstrate the performance of these 3D Kapton microfluidic devices, we selected the non-solvent-induced self-assembly of biocompatible and amphiphilic diblock copolymers. We then followed their structural evolution in situ at millisecond time scales using on-the-chip time-resolved small-angle X-ray scattering under continuous-flow conditions. Combined with complementary results from 3D finite-element method computational fluid dynamics simulations, we find that the nonsolvent mixing is mostly complete within a few tens of milliseconds, which triggers initial spherical micelle formation, while structural transitions into micelle lattices and their deswelling only occur on the hundreds of milliseconds to second time scale. These results could have an important implication for the design and formulation of amphiphilic polymer nanoparticles for industrial applications and their use as drug-delivery systems in medicine.

In this work, the mechanism of the palladium-catalysed acetoxylation of benzene C-H has been studied theoretically in detail. Based on experimental studies, a four-step mechanism for this reaction had been proposed, that is, C−H activation of benzene is the rate-determining step which forms an intermediate ( k1 pathway) which is subsequently oxidized to produce a high-valent Pd intermediate ( k2 pathway). Using quantum chemical calculations, all pathways were investigated, and the activation energy, activation enthalpy and activation Gibbs free energy for all steps were calculated and compared with each other. It was determined that the RDS proceeds through a square complex instead of a T-shaped complex. The activation energy related to the k2 pathway is higher than that of the RDS, and therefore, a new mechanism is proposed.