Iodine Sites Research Articles

Halogen-bond mediated charge transfer for visual competitive colorimetric detection of fentanyl

Colorimetric assays are inexpensive and attractive tools for the detection of fentanyl (FTN), yet further enhancing their sensitivity remains a major challenge. Herein, we develop a halogen-bond mediated visual competitive colorimetric assay for FTN using Erythrosine B (EB) as a probe. The addition of poly(ethylene oxide)-block-poly(propylene oxide)-block-poly(ethylene oxide (F-127) induces the EB aggregation, strongly suppressing the background signal. Upon the introduction of FTN, the subsequent competitive reaction displaces F-127 to generate EB-FTN charge-transfer complexes via N…I halogen bonds between electron-rich amine groups and electron-deficient iodine sites, accompanying a significant absorbance wavelength shift and pink-to-purple color change. The limits of detection of this approach for FTN are 2 mg·L−1 by the naked eye and 0.19 mg·L−1 by UV–vis spectroscopy, which are approximately 3.7-fold to 4 orders of magnitude more sensitive than the reported colorimetric assays. Meanwhile, the present method is well applied for FTN-spiked domestic sewage samples, and an easy-to-use smartphone-based digital image colorimetry is also fabricated. It is expected that such an assay can play a key role in alleviating the worldwide opioid overdose crisis.

First principles insight on enhanced photocatalytic performance of sulfur-doped bismuth oxide iodate

Bismuth oxide iodate photocatalyst is mostly limited in photocatalytic applications due to its large band gap. Doping by metal and nonmetal ions is one of the simplest and most effective ways to solve the problem. The effect mechanism of nonmetallic sulfur atoms doping on the BiOIO3 semiconductor was studied via the first principles of density functional theory (DFT). A series of doping sites were determined, and the differences in energy band structure, density of states, and light absorption spectra of BiOIO3crystals after sulfur doping were carefully investigated. The doping of any oxygen site may cause the crystal conduction band position to move down, reduce the energy band gap, and the energy required for electron transition is easier to meet, which enhances the photocatalytic activity of the semiconductor. Iodine site doping gives a more reasonable crystal formation energy than substituting oxygen site doping. Moreover, the crystal with iodine doping will introduce obvious impurity states around the Fermi level, and the impurity level can act as a bridge for the electron transition. This work is also helpful in understanding the improvement of photocatalytic performance through crystal doping modification.

Simultaneous introduction of iodine and Fe-Nx into carbon nanospheres for enhanced catalytic activity towards oxygen reduction using a solution plasma process

The oxygen reduction reaction (ORR) plays a critical role at the cathode of fuel cells and metal–air batteries. In this study, we report the one-pot synthesis of iodine- and Fe-Nx impregnated carbon nanospheres (FeNI-CNS) using a solution plasma process and their effect on electrocatalytic activity. FeNI-CNS exhibits a fast four-electron transfer reaction with a high current density and superior durability in both alkaline and acidic media. The excellent catalytic performance is attributed to the synergetic effect between the iodine and Fe-Nx sites, which provide a higher reaction rate and faster ORR, respectively. We believe that these findings represent a new approach for enhancing ORR catalytic performance and catalyst synthesis.

Metal halide coordination compounds with quinazolin-4(3H)-one.

Three coordination compounds of quinazolin-4(3H)-one (quinoz; C8H6N2O) with divalent group 12 halides are reported. In all complexes, coordination occurs via the nitro-gen atom ortho to the quinazolinone carbonyl group. In the two chain polymers with composition [MX 2(quinoz)], viz. (M = Cd, X = Br), catena-poly[[[quinazolin-4(3H)-one-κN 3]cadmium(II)]-di-μ-bromido], [CdBr2(C8H6N2O)]n (I), and M = Hg, X = Cl, catena-poly[[[quinazolin-4(3H)-one-κN 3]mercury(II)]-di-μ-chlorido], [HgCl2(C8H6N2O)]n (II), the divalent cations are five-coordinate, with four bridging halide and one terminal quinoz ligand. The CdII atom in (I) has an almost trigonal-bipyramidal coordination environment, whereas the HgII atom in (II) has a more distorted coordination environment. Likewise, the halide bridges in (II) are significantly more asymmetric than in (I). In both (I) and (II), quinoz ligands at adjacent cations along each strand are oriented in opposite directions, and the organic ligands of neighboring strands inter-digitate with resulting π-π inter-actions. In contrast to the halide-bridged chain polymers (I) and (II), the adduct of quinoz with CdI2 is the tetra-hedral complex [CdI2(quinoz)2], di-iodido-bis-[quinazolin-4(3H)-one-κN 3]cadmium(II), [CdI2(C16H12N4O2)], (III). The CdII atom in this discrete complex is located on a twofold rotation axis. Disorder in (III) is reflected in an alternative minority orientation of the mol-ecules for which the iodine sites closely match the position of the majority orientation. In view of the low site occupancy of only 0.0318 (8) Å, only the CdII position for this alternative orientation was taken into account during refinement. In all three compounds, classical N-H⋯O hydrogen bonds with donor-acceptor distances of ca 2.9 Å occur; they link the polymer chains in (I) and (II) into di-periodic networks and connect adjacent discrete complexes in (III) to mono-periodic strands.

All-XUV Pump-Probe Transient Absorption Spectroscopy of the Structural Molecular Dynamics of Di-iodomethane

In this work, we use an extreme-ultraviolet (XUV) free-electron laser (FEL) to resonantly excite the I: 4d5/2–σ* transition of a gas-phase di-iodomethane (CH2I2) target. This site-specific excitation generates a 4d core hole located at an iodine site, which leaves the molecule in a well-defined excited state. We subsequently measure the time-dependent absorption change of the molecule with the FEL probe spectrum centered on the same I: 4d resonance. Using ab initio calculations of absorption spectra of a transient isomerization pathway observed in earlier studies, our time-resolved measurements allow us to assign the timescales of the previously reported direct and indirect dissociation pathways. The presented method is thus sensitive to excited-state molecular geometries in a time-resolved manner, following a core-resonant site-specific trigger.Received 9 June 2020Revised 27 February 2021Accepted 10 May 2021DOI:https://doi.org/10.1103/PhysRevX.11.031001Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI. Open access publication funded by the Max Planck Society.Published by the American Physical SocietyPhysics Subject Headings (PhySH)Research AreasPhotodissociationPhysical SystemsMoleculesTechniquesTransient absorption spectroscopyAtomic, Molecular & Optical

Modulation of Photoinduced Iodine Expulsion in Mixed Halide Perovskites with Electrochemical Bias.

Hole trapping at iodine (I) sites in MAPbBr1.5I1.5 mixed halide perovskites (MHP) is responsible for iodine migration and its eventual expulsion into solution. We have now modulated the photoinduced iodine expulsion in MHP through an externally applied electrochemical bias. At positive potentials, electron extraction at TiO2/MHP interfaces becomes efficient, leading to hole buildup within MHP films. This improved charge separation, in turn, favors iodine migration as evident from the increased apparent rate constant of iodine expulsion (kexpulsion = 0.0030 s-1). Conversely, at negative potentials (-0.3 V vs Ag/AgCl) electron-hole recombination is facilitated within MHP, slowing down iodine expulsion by an order of magnitude (kexpulsion = 0.00018 s-1). The tuning of the EFermi level through external bias modulates electron extraction at the TiO2/MHP interface and indirectly controls the buildup of holes, ultimately inducing iodine migration/expulsion. Suppressing iodine migration in perovskite solar cells is important for attaining greater stability since they operate under internal electrical bias.

F-Centers in BaBrI Single Crystal

In this article, we demonstrate the results of experimental and theoretical studies of F-centers in BaBrI single crystals. We have observed two types of F-centers related to an electron trapped in the iodine or bromine vacancy site. It was found that absorption bands due to F-centers can be induced either by radiation or additive coloration. The excitonic mechanism of F-center production was established and demonstrated. Optical properties of the F-centers in a monoclinic symmetry environment have been calculated by means of the embedded cluster method.

Structural changes in chlorine-substituted SbSI

The antimony sulphoiodide (SbSI) is considered a prospective and important ferroelectric material due to its unique properties below Curie temperature Tc. However, the fact that current practical applications require higher working temperatures has prompted new structural improvements that extend the ferroelectric state. In this ternary system, Tc is highly sensitive to any chemical modifications or stress. Therefore, one way to adjust the Tc is through selective substitution of the constituent elements. In this work, SbSI has been fractionally chlorine-substituted at the iodine site and examined using temperature-dependent x-ray diffraction and specific heat capacity methods. Although a considerable increase in Tc has been achieved, a more detailed analysis shows that the Tc increases with x from 0 to 0.2 and starts to decrease when x > 0.2. The maximum Tc increase in the range of x = 0–0.3 is ∼15.3%. The reverse behavior, from increase to decrease, is thoroughly discussed with reference to the previously published data on SbSI1-xClx compounds.

Theoretical evidence for the sensitivity of charge-rearrangement-enhanced x-ray ionization to molecular size

It was recently discovered that molecular ionization at high x-ray intensity is enhanced, in comparison with that of isolated atoms, through a phenomenon called CREXIM (charge-rearrangement-enhanced x-ray ionization of molecules). X-ray absorption selectively ionizes heavy atoms within molecules, triggering electron transfer from neighboring atoms to the heavy atom sites and enabling further ionization there. The present theoretical study demonstrates that the CREXIM effect increases with the size of the molecule, as a consequence of increased intramolecular electron transfer from the larger molecular constituents attached to the heavy atoms. We compare x-ray multiphoton ionization dynamics of xenon, iodomethane, and iodobenzene after interacting with an intense x-ray pulse. Although their photoionization cross sections are similar, iodomethane and iodobenzene molecules are more ionized than xenon atoms. Moreover, we predict that the average total charge of iodobenzene is much larger than that of iodomethane, because of the large number of electrons in the benzene ring. The positive charges transferred from the iodine site to the benzene ring are redistributed such that the higher carbon charges are formed at the far end from the iodine site. Our first-principles calculations provide fundamental insights into the interaction of molecules with x-ray free-electron laser (XFEL) pulses. These insights need to be taken into account for interpreting and designing future XFEL experiments.

A polymerization scenario of the liquid–liquid transition of GeI4

SnI4 and GeI4 have been shown to exhibit similar polyamorphic nature. We examine the microscopic nature of the liquid–liquid transition in GeI4 by conducting an isothermal–isobaric molecular dynamics simulation for the system composed of rigid tetrahedral molecules. The model allows us to semiquantitatively discuss the structural properties of liquid GeI4 below 1 GPa. We define a physical bond between the nearest intermolecular iodine sites satisfying the conditions of forming the metallic I2 bond. We then focus on the formation of molecular clusters in dynamic networks of the bonds. The clusters are mainly formed by molecules whose nearest pairs are in edge-to-edge, face-to-edge, and vertex-to-edge orientations. The clusters grow as pressure increases, and the onset of percolation is observed below 1 GPa. The finite-size scaling analysis for the percolation probability identifies that the threshold pressure is GPa for the present model, which is near the extension of the boundary between the two liquid phases. We thus speculate that the liquid–liquid transition of GeI4 is attained by polymerization, i.e. percolation of molecular networks. The same percolation scenario with a slight modification such as introducing a bootstrap mechanism is expected to apply to the transition in liquid SnI4.

The Structure of Radiative Tunnel Recombination Sites in Emulsion Microcrystals of AgBr(I)

To identify the structure of emissive tunnel recombination sites in the emulsion microcrystals of silver bromide AgBr(I) with iodine contaminations and to determine the role of an emulsion medium in their formation, the temperature dependence of the luminescence spectra in the range from 77 to 120 K, the kinetics of the growth of the maximum luminescence intensity value at λ ≈ 560 nm, and the luminescence flash spectrum stimulated by the infrared light are investigated. Two types of the AgBr1 – x(I x ) (x = 0.03) microcrystals—namely, obtained in an aqueous solution and on a gelatin substrate—are used in the studies. It is established that the emissive tunnel recombination sites with a luminescence maximum at λ ≈ 560 nm in AgBr1 – x(I x ) (x = 0.03) are the {(I a - I a - )Ag i + } donor–acceptor complexes with the I a - iodine ions located in neighbor anionic sites of the AgBr(I) crystal lattice, next to which the Ag i + interstitial silver ion is positioned. With an increase in the temperature, the {(I a - I a - )Ag i + } sites undergo structural transformation into the {(I a - I a - )Agin+} sites, where n = 2, 3, …. Moreover, the {(I a - I a - )Ag i + } sites (n = 2) after the capture of an electron and hole also provide the tunnel recombination with a luminescence maximum at λ ≈ 720 nm. The influence of an emulsion medium consists in that gelatin interacts with the surface electron-localization sites, i.e., the interstitial silver ions Ag i + , n = 1, 2, and forms the complexes {Ag i 0 G+} (n = 1, 2) with them. The latter are deeper electron traps with a small capture cross section as compared to the Ag i + sites (n = 1, 2) and that manifest themselves in that the kinetics of the luminescence growth in AgBr(I) to a stationary level at λ ≈ 560 nm is characterized by the presence of “flash firing.” At the same time, the luminescence flash stimulated by IR light, for which the Ag i + (n = 1, 2) electron-localization sites are responsible, is absent. It is supposed that the electrons localized on the {Ag i + G+} complexes (n = 2) retain the capability for emissive tunnel recombination with holes localized on paired iodine sites with a luminescence maximum at λ ≈ 750 nm.

Femtosecond charge and molecular dynamics of I-containing organic molecules induced by intense X-ray free-electron laser pulses.

We studied the electronic and nuclear dynamics of I-containing organic molecules induced by intense hard X-ray pulses at the XFEL facility SACLA in Japan. The interaction with the intense XFEL pulse causes absorption of multiple X-ray photons by the iodine atom, which results in the creation of many electronic vacancies (positive charges) via the sequential electronic relaxation in the iodine, followed by intramolecular charge redistribution. In a previous study we investigated the subsequent fragmentation by Coulomb explosion of the simplest I-substituted hydrocarbon, iodomethane (CH3I). We carried out three-dimensional momentum correlation measurements of the atomic ions created via Coulomb explosion of the molecule and found that a classical Coulomb explosion model including charge evolution (CCE-CE model), which accounts for the concerted dynamics of nuclear motion and charge creation/charge redistribution, reproduces well the observed momentum correlation maps of fragment ions emitted after XFEL irradiation. Then we extended the study to 5-iodouracil (C4H3IN2O2, 5-IU), which is a more complex molecule of biological relevance, and confirmed that, in both CH3I and 5-IU, the charge build-up takes about 10 fs, while the charge is redistributed among atoms within only a few fs. We also adopted a self-consistent charge density-functional based tight-binding (SCC-DFTB) method to treat the fragmentations of highly charged 5-IU ions created by XFEL pulses. Our SCC-DFTB modeling reproduces well the experimental and CCE-CE results. We have also investigated the influence of the nuclear dynamics on the charge redistribution (charge transfer) using nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulation. The time scale of the charge transfer from the iodine atomic site to the uracil ring induced by nuclear motion turned out to be only ∼5 fs, indicating that, besides the molecular Auger decay in which molecular orbitals delocalized over the iodine site and the uracil ring are involved, the nuclear dynamics also play a role for ultrafast charge redistribution. The present study illustrates that the CCE-CE model as well as the SCC-DFTB method can be used for reconstructing the positions of atoms in motion, in combination with the momentum correlation measurement of the atomic ions created via XFEL-induced Coulomb explosion of molecules.

On the structural basis of the presence of two optical axes in α-HIO3 crystal

An X-ray diffraction study of α-HIO3 crystal has been performed with the following results: sp. gr. P212121, Z = 4, a = 5.5360(3) A, b = 5.8723(6) A, c = 7.7291(5) A, and R factors R(F)/wR(F) = 0.86/0.69%. Disordering of iodine site is revealed, which is described in terms of anharmonic atomic displacements. Packing (likely unique) of all structure atoms over two systems of planes rotated by an angle close to the rotation of optical axes (47°) is revealed. The rotation of the plane of polarization of light based on the structural data is calculated for the first time for the α-HIO3 crystal.

Exploring Supramolecular Self-Assembly of Metalloporphyrin Tectons by Halogen Bonding. 2

In expansion of earlier observations, one SnIV(L)2, one oxo–VIV, and nine oxo–MoV(L) new porphyrin compounds (L = anionic axial ligand) have been synthesized and structurally characterized by single crystal X-ray diffraction analysis to probe the occurrence of halogen bonds in crystalline metalloporphyrin assemblies. The [Sn(TIPP)(p-NO2-phenolate)2] six-coordinate system (TIPP = dianion of 5,10,15,20-meso-tetrakis(4-iodophenyl)porphyrin) (1) exhibits weak I···O interactions, stimulating further studies with the oxo–Mo/V porphyrin scaffolds. The domed complex [V(O)(TIPP)] (2) crystallizes in a chiral space group and shows short O···π contacts along the polar axis, but no distinct halogen bonds. In [Mo(O)(TIPP)(L)] (L = 1-hydroxybenzotriazolate (3), 5-bromonicotinate (4), pyrimidine-5-carboxylate (5), 4-iodobenzoate (6), 2-chlorobenzoate (7)) diverse (O···I, N···I, I···I) halogen bonds and halogen-bonding-type contacts have been observed, depending upon the nature of the axial ligand attached to the Mo center. In analogous compounds with TBrPP, [Mo(O)(TBrPP)(L)] (TBrPP = dianion of 5,10,15,20-meso-tetrakis(4-bromophenyl)porphyrin, L = 5-bromonicotinate (8), isonicotinate (9)), directional halogen interactions involving bromine have not been detected. Intermolecular N···I halogen bonding has also been observed when the N-donor sites were positioned on the porphyrin periphery and the iodine acceptor on the axial ligand as in [Mo(O)(T4pyP)(4-iodobenzoate)] (10) (T4pyP = dianion of 5,10,15,20-meso-tetrakis(4-pyridyl)porphyrin). An attempt to induce the formation of halogen bonded chain assemblies through I···O interaction between the axial oxo and iodine sites of adjacent species in [Mo(O)(TTP)(4-iodobenzoate)] (11) (TTP = dianion of 5,10,15,20-meso-tetrakis(p-tolyl)porphyrin) has not been successful.

Structural tunability and switchable exciton emission in inorganic-organic hybrids with mixed halides

Room-temperature tunable excitonic photoluminescence is demonstrated in alloy-tuned layered Inorganic-Organic (IO) hybrids, (C12H25NH3)2PbI4(1−y)Br4y (y = 0 to 1). These perovskite IO hybrids adopt structures with alternating stacks of low-dimensional inorganic and organic layers, considered to be naturally self-assembled multiple quantum wells. These systems resemble stacked monolayer 2D semiconductors since no interlayer coupling exists. Thin films of IO hybrids exhibit sharp and strong photoluminescence (PL) at room-temperature due to stable excitons formed within the low-dimensional inorganic layers. Systematic variation in the observed exciton PL from 510 nm to 350 nm as the alloy composition is changed, is attributed to the structural readjustment of crystal packing upon increase of the Br content in the Pb-I inorganic network. The energy separation between exciton absorption and PL is attributed to the modified exciton density of states and diffusion of excitons from relatively higher energy states corresponding to bromine rich sites towards the lower energy iodine sites. Apart from compositional fluctuations, these excitons show remarkable reversible flips at temperature-induced phase transitions. All the results are successfully correlated with thermal and structural studies. Such structural engineering flexibility in these hybrids allows selective tuning of desirable exciton properties within suitable operating temperature ranges. Such wide-range PL tunability and reversible exciton switching in these novel IO hybrids paves the way to potential applications in new generation of optoelectronic devices.

Surface concentration dependent structures of iodine on Pd(110)

We use photoelectron spectroscopy, low energy electron diffraction, scanning tunneling microscopy, and density functional theory to investigate coverage dependent iodine structures on Pd(110). At 0.5 ML (monolayer), a c(2 × 2) structure is formed with iodine occupying the four-fold hollow site. At increasing coverage, the iodine layer compresses into a quasi-hexagonal structure at 2∕3 ML, with iodine occupying both hollow and long bridge positions. There is a substantial difference in electronic structure between these two iodine sites, with a higher electron density on the bridge bonded iodine. In addition, numerous positively charged iodine near vacancies are found along the domain walls. These different electronic structures will have an impact on the chemical properties of these iodine atoms within the layer.

An anomaly in the isotopomer shift of the hyperfine spectrum of LiI

A high-precision examination of the hyperfine spectrum of 6LiI in comparison with 7LiI shows a shift in the iodine nuclear electric quadrupole moment that cannot be accounted for by a model in which the electric field gradient at the iodine site is assumed to depend only upon the internuclear distance between Li and I. The other hyperfine interactions are consistent between the two isotopomers, including the previously reported electric hexadecapole interaction of the iodine nucleus.

Crystal structure of human SH3BGRL protein: The first structure of the human SH3BGR family representing a novel class of thioredoxin fold proteins

Introduction. The humanSH3BGRL (h-SH3BGRL) gene is a member of the human SH3BGR family. The human SH3BGR (SH3 binding glutamic acid-rich) gene was cloned and characterized in 1997 in an effort to identify new genes located to chromosome 21. After the characterization of SH3BGR, three novel human genes, h-SH3BGRL, h-SH3BGRL2, and h-SH3BGRL3, were identified, showing a high homology to the N-terminal region of the h-SH3BGR protein. They are therefore believed to be a new family of human gene, the h-SH3BGR gene family. The h-SH3BGRL gene located to chromosome Xq13.3 encodes for a small protein of 114 amino acids, which is apparently widely expressed in many tissues including liver and blood. The h-SH3BGRLprotein features a prolinerich sequence (PLPPQIF), which contains both the SH3 binding (PXXP) and the Homer EVH1 binding (PPXXF) motif. This proline-rich region is highly conserved in h-SH3BGR family and was expected to be functionally important. Although it is known that the SH3BGRL gene is missing in a mentally retarded male patient, the exact functional role of h-SH3BGRL is still needed to be defined. Here we report the crystal structure of h-SH3BGRL protein determined by the SIRAS method. The structure indicates that SH3BGRL can not bind to the SH3 or Homer EVH1 domain as previously expected due to our finding that the binding motif (PLPPQIF) is buried in the tertiary structure. As the first structure of the human SH3BGR protein family, the tertiary structure of h-SH3BGRL shows a typical thioredoxin fold at the Nterminal part and a helix-loop-helix motif at the Cterminal lobe. Sequence and structure comparisons show that h-SH3BGRL belongs to the thioredoxin fold protein family but it is distinct from all five classes of the thioredoxin fold proteins identified thus far. According to the unique structural and functional characterizations, h-SH3BGRL represents a novel class of the thioredoxin fold proteins.

Structural Basis for Metal Ion Coordination and the Catalytic Mechanism of Sphingomyelinases D

Sphingomyelinases D (SMases D) from Loxosceles spider venom are the principal toxins responsible for the manifestation of dermonecrosis, intravascular hemolysis, and acute renal failure, which can result in death. These enzymes catalyze the hydrolysis of sphingomyelin, resulting in the formation of ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidyl choline, generating the lipid mediator lysophosphatidic acid. This report represents the first crystal structure of a member of the sphingomyelinase D family from Loxosceles laeta (SMase I), which has been determined at 1.75-angstrom resolution using the "quick cryo-soaking" technique and phases obtained from a single iodine derivative and data collected from a conventional rotating anode x-ray source. SMase I folds as an (alpha/beta)8 barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface. Substrate binding and/or the transition state are stabilized by a Mg2+ ion, which is coordinated by Glu32, Asp34, Asp91, and solvent molecules. In the proposed acid base catalytic mechanism, His12 and His47 play key roles and are supported by a network of hydrogen bonds between Asp34, Asp52, Trp230, Asp233, and Asn252.

Effects of adsorbates on charge exchange in Li+ ion scattering from Ni(100)

Resonant charge transfer during the backscattering of 3.0 keV Li+ from hydrogen- and iodine-covered Ni(100) is probed with time-of-flight spectroscopy. Hydrogen adsorption on Ni(100) induces only a small increase of the surface work function and the neutralization probabilities for backscattered Li are not significantly affected. Iodine adsorbs with some net negative charge, so that a dipole directed into the surface is expected. Such a dipole would increase the work function thereby decreasing the neutralization probability. Iodine adsorption decreases the work function of Ni(100), however, and the neutralization probabilities for Li scattered from the iodine sites are always larger than for scattering from nickel sites. These results suggest that the local charge density associated with adsorbed iodine is not uniform.