Unambiguous Assignment Research Articles

Application of Relay C−H Oxidation Logic to Polyhydroxylated Oleanane Triterpenoids

Summary Although clinical applications of abundant feedstock triterpenoids such as oleanolic acid are limited because of poor solubility and bioavailability, synthetic access to higher hydroxylated oleanane terpenoids is challenging. We now report the use of relay C−H oxidation logic to mimic the processes carried out in nature by P450 monooxygenase enzymes. To this end, we used the C-23-OH as natural handle for a hydrogen-atom transfer to access C-6, enabling the first syntheses of highly oxidized natural products uncargenin C and protobassic acid as well as uncovering the anti-leukemic activity of a synthetic intermediate.

Evaluation of NHS-Acetate and DEPC labelling for determination of solvent accessible amino acid residues in protein complexes

The activity of most proteins and protein complexes relies on the formation of defined three-dimensional structures. The analysis of these arrangements is therefore key for understanding their function and regulation in the cell. Besides the traditional structural techniques, structural mass spectrometry delivers insights into the various aspects of protein structure, including stoichiometry, protein-ligand interactions and solvent accessibility. The latter is usually obtained from labelling experiments. In this study, we evaluate two chemical labelling strategies using N-hydroxysuccinimidyl acetate and diethylpyrocarbonate as labelling reagents. We characterised the mass spectra of modified peptides and assessed labelling reactivity of individual amino acid residues in intact proteins. Importantly, we uncovered neutral losses from diethylpyrocarbonate modified amino acids improving the assignments of the peptide fragment spectra. We further established a quantitative labelling workflow to determine labelling percentage and unambiguously distinguish solvent accessible amino acid residues from stochastically labelled residues. Finally, we used ion mobility MS to explore whether labelled proteins maintain their structures and remain stable. We conclude that labelling using N-hydroxysuccinimidyl acetate and diethylpyrocarbonate delivers comparable results, however, N-hydroxysuccinimidyl acetate labelling is compatible with standard proteomic workflows while diethylpyrocarbonate labelling requires specialised experimental conditions and data analysis. SignificanceCovalent labelling is widely used to identify solvent accessible amino acid residues of proteins or protein complexes. However, with increasing sensitivity of available MS instrumentation, a high number of modified residues is usually observed making an unambiguous assignment of solvent accessible residues necessary. In this study, we establish a quantitative labelling workflow for two different labelling strategies to identify accessible amino acid residues. In addition, we characterise observed mass spectra of modified peptides and identified neutral loss of DEPC modified amino acid residues during HCD fragmentation improving their assignments.

Lattice dynamics in the spin- 12 frustrated kagome compound herbertsmithite

We investigate the lattice dynamics in the spin-1/2 frustrated kagome compound herbertsmithite ZnCu$_3$(OH)$_6$Cl$_2$ by a combination of infrared spectroscopy measurements and ab initio density functional theory calculations, and provide an unambiguous assignment of infrared-active lattice vibrations involving in-plane and out-of-plane atom displacements in the kagome layers. Upon cooling, non-thermal red-shifts and broadening appear specifically for modes that deform the kagome layer or affect the Cu-O-Cu bond angles, thus creating pronounced modifications of the antiferromagnetic exchange coupling. Our results indicate the presence of a strong magnetoelastic coupling to the spin system. We discuss the effects of this coupling and its relation to recent experiments reporting a global symmetry reduction of the kagome lattice symmetry.

New rotational analysis of the 010-010 and 000–010 bands in the A[formula omitted] - X2Π electronic transition of the N2O[formula omitted] molecule

In this work a new analysis of the 010-010 and 000–010 bands in the A2Σ+ - X2Π electronic transition of the N2O+ molecule is performed by high resolution Fourier transform spectroscopy. Two sets of spectra of the N2O+ molecule at different temperatures are analysed, one at 30 K and the other at 340 K approximately, which made possible an unambiguous assignment of the spectral lines. Due to this fact and from a “natural” advantage of the Fourier transform spectroscopy since, being an interferential spectrometry, the obtained spectrum provides absolute wavenumbers and no further calibration is required, the more accurate wavenumber allowed new and improved molecular constants and band origins, making it possible to obtain more reliable values for previously reported molecular constants. With these new constants, a new set of spin-vibronic term values was determined and compared to the values already reported in the literature.

Computational and Spectroscopic Studies of Carbon Disulfide.

The vibrational spectroscopy of CS2 has been investigated many times in all three phases. However, there is still some ambiguity about the location of two of the modes in the solid state. The aim of this work was to locate all of the modes by inelastic neutron scattering (INS) spectroscopy, (which has no selection rules), and to use periodic density functional theory to provide a complete and unambiguous assignment of all the modes in the solid state. A comparison of the observed and calculated INS spectra shows generally good agreement. All four of the ν2 bending mode components are calculated to fall within 14 cm−1. Inspection of the spectrum shows that there are no bands close to the intense feature at 390 cm−1 (assigned to ν2); this very strongly indicates that the Au mode is within the envelope of the 390 cm−1 band. Based on a simulation of the band shape of the 390 cm−1 feature, the most likely position of the optically forbidden component of the ν2 bending mode is 393 ± 2 cm−1. The calculations show that the optically inactive Au translational mode is strongly dispersed, so it does not result in a single feature in the INS spectrum.

Development of a Non-Targeted Method to Study Petroleum Polyaromatic Hydrocarbons in Soil by Ultrahigh Resolution Mass Spectrometry Using Multiple Ionization Methods

A non-targeted method for analyzing petroleum hydrocarbons in soil was established by extracting a wide range of PAC compounds using a model system. Here, sand was spiked with a heavy crude oil, which simulated a hydrocarbon contaminated soil of low soil organic matter (SOM). Soxhlet and supercritical fluid extraction (SFE) was optimized for PAXHs analysis in soil. A concept of using multidimensional ionization for ultrahigh resolution mass spectrometry was employed for detection using electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI) and atmospheric pressure photo ionization (APPI) for the analysis of polycyclic aromatic hydrocarbons (PAHs) and polycyclic aromatic heterocycles. Fourier transform mass spectrometry (FT-MS) with its ultrahigh mass resolution and high mass accuracy enables an unambiguous assignment of the detected ions obtained from different ionization methods, which provides a secure and comprehensive view of contaminants in soil on a molecular level. Over 95% of the spiked crude oil could be recovered by Soxhlet extraction using toluene, dichloromethane and acetone:n-hexane (1:1, v:v). In comparison, when using SFE with supercritical CO2 the recovery was only about 50% but showed more polar compounds. Detailed analyses showed that besides 16 PAHs, a wide range with more than 10,000 PAXHs could also be successfully extracted.

High-resolution infrared spectroscopy of jet cooled CH2Br radicals: The symmetric CH stretch manifold and absence of nuclear spin cooling.

Direct laser absorption of a slit supersonic discharge expansion provides the first high-resolution spectroscopic results on the symmetric CH stretch excitation (ν1) of the bromomethyl (CH2Br) radical in the ground electronic state. Narrowband (<1 MHz) mid-infrared radiation is produced by difference-frequency generation of two visible laser beams, with the open shell halohydrocarbon radical generated by electron dissociative attachment of CH2Br2 in a discharge and rapidly cooled to Trot = 18 ± 1 K in the subsequent slit-jet supersonic expansion. A rovibrational structure in the radical spectrum is fully resolved, as well as additional splittings due to spin-rotation effects and 79Br/81Br isotopologues in natural abundance. Spectroscopic constants and band origins are determined by fitting the transition frequencies to a non-rigid Watson Hamiltonian, yielding results consistent with a vibrationally averaged planar radical and an unpaired electron in the out-of-plane pπ orbital. Additionally, extensive satellite band structure from a vibrational hot band is observed and analyzed. The hot band data is compared to CFOUR/VPT2 (CCSD(T)cc-pVQZ) ab initio anharmonic predictions of the vibration rotation alpha matrix, which permits unambiguous assignment to CH2 symmetric-stretch excitation built on the singly excited CH2 out-of-plane bending mode (ν1 + ν4 ← ν4). Longitudinal cooling of the Doppler width in the slit-jet expansion geometry also reveals partially resolved hyperfine structure on transitions out of the lowest angular momentum states in excellent agreement with predictions based on microwave studies. High level ab initio MOLPRO calculations [CCSD(T)-f12b/VnZ-f12 (n = 3, 4, CBS)] are also performed with explicitly correlated f12 electron methods for the out-of-plane CH2 bending mode over the halogen series CH2X (X = F, Cl, Br, I), which clearly reveals a non-planar geometry for X = F (with a ΔE ≈ 0.3 kcal/mol barrier) and yet planar equilibrium geometries for X = Cl, Br, and I. Finally, a detailed Boltzmann analysis of the transition intensities provides support for negligible collisional equilibration of the entangled H atom nuclear spin states on the few hundred microsecond time scale and high collision densities of a slit supersonic expansion.

Heterotrimetallic Mixed‐Valent Molecular Precursors Containing Periodic Table Neighbors: Assignment of Metal Positions and Oxidation States

AbstractA known trinuclear structure was used to design the heterobimetallic mixed‐valent, mixed‐ligand molecule [CoII(hfac)3−Na−CoIII(acac)3] (1). This was used as a template structure to develop heterotrimetallic molecules [CoII(hfac)3−Na−FeIII(acac)3] (2) and [NiII(hfac)3−Na−CoIII(acac)3] (3) via isovalent site‐specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple‐wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di‐ and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM′O4 functional oxide materials.

Determination of the Composition of LDPE/LLDPE Blends via 13C NMR

AbstractPolyethylene film properties can be manipulated by blending linear low‐density polyethylene (LLDPE) with low density polyethylene (LDPE) resin. The accurate determination of LDPE content in those blends, however, is challenging. Differential scanning calorimetry analysis has been traditionally used to determine the LDPE content, but the result can have significant error due to several limitations. Due to co‐crystallization, significant error can also result using temperature rising elution fractionation technique. In principle, the LDPE content would be determined by 13C NMR analysis if the short‐chain branch (SCB) content of the LDPE could be determined accurately. But unambiguous assignment of all peaks in the 13C NMR spectrum of a LDPE is difficult, if possible. Consequently, the SCB content of LDPE cannot be determined accurately. Therefore, a new approach is required to analyze the LDPE/LLDPE blend composition by 13C NMR on a routine basis. In this paper, a robust 13C NMR method to determine the LDPE content in LDPE/LLDPE blends is presented. By identifying unique LDPE peaks in the 13C NMR spectrum of a LDPE/LLDPE blend compared to that of LLDPE, the blend composition can be determined. The accuracy and precision of this method will also be discussed.

Heterotrimetallic Mixed‐Valent Molecular Precursors Containing Periodic Table Neighbors: Assignment of Metal Positions and Oxidation States

A known trinuclear structure was used to design the heterobimetallic mixed-valent, mixed-ligand molecule [CoII (hfac)3 -Na-CoIII (acac)3 ] (1). This was used as a template structure to develop heterotrimetallic molecules [CoII (hfac)3 -Na-FeIII (acac)3 ] (2) and [NiII (hfac)3 -Na-CoIII (acac)3 ] (3) via isovalent site-specific substitution at either of the cobalt positions. Diffraction methods, synchrotron resonant diffraction, and multiple-wavelength anomalous diffraction were applied beyond simple structural investigation to provide an unambiguous assignment of the positions and oxidation states for the periodic table neighbors in the heterometallic assemblies. Molecules of 2 and 3 are true heterotrimetallic rather than a statistical mixture of two heterobimetallic counterparts. Trinuclear platform 1 exhibits flexibility in accommodating a variety of di- and trivalent metals, which can be further utilized in the design of molecular precursors for the NaMM'O4 functional oxide materials.

Molecular sexing is a viable alternative to probing for determining sex in the imperiled Louisiana Pine Snake (Pituophis ruthveni)

Determining sex is critical for demographic monitoring of endangered species, but this task can be particularly challenging in reptiles that are sexually monomorphic. Conventional sexing methods are invasive, often inaccurate, can cause injury, and, for sexually immature individuals, equivocal. Molecular approaches have been established as viable alternatives but have not been compared with conventional methods. Here we compare the performance of cloacal probing with a molecular genetic approach to determine sex in Louisiana Pine Snakes. This highly endangered species is rare, cryptic, and largely fossorial, presenting particular difficulties for assessing their population status. Molecular assays produced unambiguous sex assignments for all individuals, whereas probing recovered an incorrect or unidentified sex 28% of the time. These results reveal that molecular sexing outperforms probing for determining sex in Louisiana Pine Snakes, suggesting management programs for other snakes of conservation concern could benefit by incorporating similar genetic approaches.

Legal aspects of synchronising data on real property location in polish cadastre and land and mortgage register

In recent years, many attempts have been made in Poland to enable automatic data exchange between the system of the Cadastre, being the responsibility of local government units, and the system of Land and Mortgage Register, maintained by the judicial administration (supported by the state apparatus represented by the Ministry of Justice). Such exchange is necessary as it is dictated by the establishment of the Integrated Real Estate Information System. These actions, however, are hindered by the different approaches of the users to the designs and functions of the two systems, as well as by the data incompatibility between the two registers.The article discusses various categories of problems related to the need to synchronise the terms corresponding to spatial objects between individual groups of users. Then, it outlines the difficulties associated with the unambiguous assignment of spatial objects to specific objects of a higher hierarchy level, resulting from the different priorities of the operators of both systems.The author also points out to the fact that ensuring coherence of the data on real property location is yet another condition allowing automatic data exchange between the systems and a full data modernization process in the base systems for the Integrated Real Estate Information System. Due to significant discrepancies between the assumptions of the systems and the data actually stored in them, such systematisation of attributes is necessary. The process of making the data on real estate consistent must take into account the conditions related to both historical events, often dating back to the times of partitions, as well as errors repeatedly committed on current basis, related to the incorrect entry of new data. The article has also pointed to the problems in data standardisation, resulting from multi-level administrative divisions, carried out due to various social needs.

Vibrational Dynamics of Crystalline 4-Phenylbenzaldehyde from INS Spectra and Periodic DFT Calculations.

The present work emphasizes the value of periodic density functional theory (DFT) calculations in the assessment of the vibrational spectra of molecular crystals. Periodic calculations provide a nearly one-to-one match between the calculated and observed bands in the inelastic neutron scattering (INS) spectrum of crystalline 4-phenylbenzaldehyde, thus validating their assignment and correcting previous reports based on single molecule calculations. The calculations allow the unambiguous assignment of the phenyl torsional mode at ca. 118–128 cm−1, from which a phenyl torsional barrier of ca. 4000 cm−1 is derived, and the identification of the collective mode involving the antitranslational motion of CH···O bonded pairs, a hallmark vibrational mode of systems where C-H···O contacts are an important feature.

Charge‐Tagged DNA Radicals in the Gas Phase Characterized by UV/Vis Photodissociation Action Spectroscopy

AbstractAdenosine radicals tagged with a fixed‐charge group were generated in the gas phase and structurally characterized by tandem mass spectrometry, deuterium labeling, and UV/Vis action spectroscopy. Experimental results in combination with Born–Oppenheimer molecular dynamics, ab initio, and excited‐state calculations led to unambiguous assignment of adenosine radicals as N‐7 hydrogen atom adducts. The charge‐tagged radicals were found to be electronically equivalent to natural DNA nucleoside radicals.

Charge-Tagged DNA Radicals in the Gas Phase Characterized by UV/Vis Photodissociation Action Spectroscopy.

Adenosine radicals tagged with a fixed-charge group were generated in the gas phase and structurally characterized by tandem mass spectrometry, deuterium labeling, and UV/Vis action spectroscopy. Experimental results in combination with Born-Oppenheimer molecular dynamics, ab initio, and excited-state calculations led to unambiguous assignment of adenosine radicals as N-7 hydrogen atom adducts. The charge-tagged radicals were found to be electronically equivalent to natural DNA nucleoside radicals.

Surface Termination of CsPbBr3 Perovskite Quantum Dots Determined by Solid-State NMR Spectroscopy.

Cesium lead halide perovskite quantum dots (QDs) have gained significant attention as next-generation optoelectronic materials; however, their properties are highly dependent on their surface chemistry. The surfaces of cuboidal CsPbBr3 QDs have been intensively studied by both theoretical and experimental techniques, but fundamental questions still remain about the atomic termination of the QDs. The binding sites and modes of ligands at the surface remain unproven. Herein, we demonstrate that solid-state NMR spectroscopy allows the unambiguous assignment of organic surface ligands via 1H, 13C, and 31P NMR. Surface-selective 133Cs solid-state NMR spectra show the presence of an additional 133Cs NMR signal with a unique chemical shift that is attributed to Cs atoms terminating the surface of the particle and which are likely coordinated by carboxylate ligands. Dipolar dephasing curves that report on the distance between the surface ammonium ligands and Cs and Pb were recorded using double resonance 1H{133Cs} RESPDOR and 1H{207Pb} S-REDOR experiments. Model QD surface slabs with different possible surface terminations were generated from the CsPbBr3 crystal structure, and theoretical dipolar dephasing curves considering all possible 1H-133Cs/207Pb spin pairs were then calculated. Comparison of the calculated and experimental dephasing curves indicates the particles are CsBr terminated (not PbBr2 terminated) with alkylammonium ligands substituting into some surface Cs sites, consistent with the surface-selective 133Cs NMR experiments. These results highlight the utility of high-resolution solid-state NMR spectroscopy for studying ligand binding and the surface structure of nanomaterials.

Simulating the Nonadiabatic Relaxation Dynamics of 4-(N,N-Dimethylamino)benzonitrile (DMABN) in Polar Solution.

The compound 4-(N,N-dimethylamino)benzonitrile (DMABN) represents the archetypal system for dual fluorescence, a rare photophysical phenomenon in which a given fluorophore shows two distinct emission bands. Despite extensive studies, the underlying mechanism remains the subject of debate. In the present contribution, we address this issue by simulating the excited-state relaxation process of DMABN as it occurs in polar solution. The potential energy surfaces for the system are constructed with the use of the additive quantum mechanics/molecular mechanics (QM/MM) method, and the coupled dynamics of the electronic wave function and the nuclei is propagated with the semiclassical fewest switches surface hopping method. The DMABN molecule, which comprises the QM subsystem, is treated with the use of the second-order algebraic diagrammatic construction (ADC(2)) method with the imposition of spin-opposite scaling (SOS). It is verified that this level of theory achieves a realistic description of the excited-state potential energy surfaces of DMABN. The simulation results qualitatively reproduce the main features of the experimentally observed fluorescence spectrum, thus allowing the unambiguous assignment of the two fluorescence bands: the normal band is due to the near-planar locally excited (LE) structure of DMABN, while the so-called "anomalous" second band arises from the twisted intramolecular charge transfer (TICT) structure. The transformation of the LE structure into the TICT structure takes place directly via intramolecular rotation, and is not mediated by another excited-state structure. In particular, the oft-discussed rehybridized intramolecular charge transfer (RICT) structure, which is characterized by a bent nitrile group, does not play a role in the relaxation process.

Investigation of Structures, FTIR, FT-Raman, In Vivo Anti-Inflammatory, Molecular Docking and Molecular Characteristics of 2-Amino-3-Pyridine Carboxaldehyde and Its Copper(II) Complex Using Experimental and Theoretical Approach

In this work, the FT-Raman and FTIR spectra of synthesized molecules, 2-amino-3-pyridine carboxaldehyde (APC) and Cu(II) complex of 2-amino-3-pyridine carboxaldehyde (Cu(II)APC) were characterized by using density functional theory (DFT). The optimized structural parameters such as harmonic vibrational frequencies, general valence force field, infrared and Raman intensities, frontier molecular orbital parameters, NLO properties, NBO and MESP were calculated using B3LYP functional with 6-311++G(d,p) basis set. Employing MOLVIB 7.0 program, the scaling process was engaged to reach a good agreement between experimental and computed frequencies. The rms error between the scaled calculated and experimental frequencies was found at 9.1 and 10.3 cm– 1 . Unambiguous vibrational assignments were reported by using potential energy distribution (PED) and eigenvectors. APC and Cu(II)APC were evaluated for their anti-inflammatory activity using the carrageenan-induced paw oedema method. Cu(II)APC complex exhibited significant activity compared to standard drug. Molecular docking results support the anti-inflammatory activity of the title compounds against the target protein cyclooxygenase-2 (COX-2) possess the good binding energy values of –4.50 and –7.67 kcal/mol, respectively.

Photography can determine the sex of a predator with limited sexual dimorphism: A case study of the powerful owl

The ability to distinguish (in the field) the sex of wildlife that show limited sexual dimorphism is, at best, challenging but is nonetheless essential to ensure appropriate conservation strategies are implemented. We developed a technique using highly varied images, similar to those taken by amateur photographers, to accurately sex individual powerful owls (Ninox strenua) through the measurement of facial features. Powerful owls show extremely limited sexual dimorphism and have been almost impossible to sex without genetic analysis, however, we report a process that results in the unambiguous assignment of sex. Image selection was extremely important; images where the owl’s head and body faced towards the camera, in an alert posture, were selected. We derived five facial features (inter-nostril distance, inter-eye distance, head width, forehead height and facemask), all measured in pixels to account for variation in the resolution and the size of images. Ratios were then produced from these facial features enabling standardised metrics, which we tested with regard to the assignment of sex. Logistic regression analysis indicated that the ratio of head width to the inter-nostril distance was the key sexually diagnostic relationship, giving 100% accuracy in sex determination (assessed against known-sex birds). We also identified a sex-specific plumage character; where facemask feathers protrude beyond the profile of the contour feathers of the head, the bird was a female, whereas when these feathers did not protrude beyond the profile, the bird was a male. For powerful owls, simple image analysis reliably determines the sex of individuals and has potential as an extremely cost efficient approach, that can provide essential information on species dynamics such as sex ratios, social organization and behaviour. The use of photographic images is especially beneficial for species that are cryptic or are extremely difficult to capture. The quantification and analysis of images captured by amateurs enables a greater contribution of citizen scientists to conservation research.

Genetically Encodable Contrast Agents for Optical Coherence Tomography.

Optical coherence tomography (OCT) has gained wide adoption in biological research and medical imaging due to its exceptional tissue penetration, 3D imaging speed, and rich contrast. However, OCT plays a relatively small role in molecular and cellular imaging due to the lack of suitable biomolecular contrast agents. In particular, while the green fluorescent protein has provided revolutionary capabilities to fluorescence microscopy by connecting it to cellular functions such as gene expression, no equivalent reporter gene is currently available for OCT. Here, we introduce gas vesicles, a class of naturally evolved gas-filled protein nanostructures, as genetically encodable OCT contrast agents. The differential refractive index of their gas compartments relative to surrounding aqueous tissue and their nanoscale motion enables gas vesicles to be detected by static and dynamic OCT. Furthermore, the OCT contrast of gas vesicles can be selectively erased in situ with ultrasound, allowing unambiguous assignment of their location. In addition, gas vesicle clustering modulates their temporal signal, enabling the design of dynamic biosensors. We demonstrate the use of gas vesicles as reporter genes in bacterial colonies and as purified contrast agents in vivo in the mouse retina. Our results expand the utility of OCT to image a wider variety of cellular and molecular processes.