Crystallographic Distances Research Articles

Cost-Effective Hydrothermal Synthesis of Luminescent Carbon Dots from Date Palm Midrib

Nanocarbon synthesis from diverse sources has garnered significant attention, with a particular focus on materials derived from biomass. Carbon dots (CDs), due to their water solubility, low toxicity, and biocompatibility, have emerged as promising candidates for a wide range of applications. In recent years, CDs have found utility in several applications such as bioimaging, drug delivery, and biosensors. In this study, we present an eco-friendly, straightforward, and cost-effective technique for the synthesis of carbon dots through a hydrothermal reaction, utilizing peeled date palm midribs as the source material. High-resolution transmission electron microscopy, X-ray diffraction, UV-visible absorption spectroscopy, photoluminescence analysis, Fourier-transform infrared spectroscopy, and zeta potential measurements services to investigate the synthesized carbon dots' morphology, crystal and structure, and optical properties. The results show that the carbon dots had a size distribution ranging from 2.5 to 6 nm, and a crystallographic interplanar distance of 0.23 nm corresponding to the graphitic structure. When excited at a wavelength of 340 nm, the synthesized dots exhibited a prominent bluish emission at 420 nm, highlighting their potential for use in optical and biological applications. This work underscores the feasibility of harnessing sustainable biomass sources, such as date palm midribs, for the green synthesis of carbon dots with desirable properties, opening up new avenues for their utilization in cutting-edge technologies.

Inorganic synthesis-structure maps in zeolites with machine learning and crystallographic distances

Crystallographic representations and machine learning predict inorganic synthesis conditions for arbitrary zeolites, as validated with literature-mined data.

Determination of the Distance between the Mo(V) and Fe(III) Heme Centers of Wild Type Human Sulfite Oxidase by Pulsed EPR Spectroscopy

Intramolecular electron transfer (IET) between the molybdenum and heme centers of vertebrate sulfite oxidase (SO) is proposed to be a key step in the catalytic cycle of the enzyme. However, the X-ray crystallographic distance between these centers, R(MoFe) = 32.3 Å, appears to be too long for the rapid IET rates observed in liquid solution. The Mo and heme domains are linked by a flexible tether, and it has been proposed that dynamic interdomain motion brings the two metal centers closer together and thereby facilitates rapid IET. To date, there have been no direct distance measurements for SO in solution that would support or contradict this model. In this work, pulsed electron-electron double resonance (ELDOR) and relaxation induced dipolar modulation enhancement (RIDME) techniques were used to obtain information about R(MoFe) in the Mo(V)Fe(III) state of wild type recombinant human SO in frozen glassy solution. Surprisingly, the data obtained suggest a fixed structure with R(MoFe) = 32 Å, similar to that determined by X-ray crystallography for chicken SO, although the orientation of the R(MoFe) radius-vector with respect to the heme center was found to be somewhat different. The implications of these findings for the flexible tether model are discussed.

Detecting Intramolecular Conformational Dynamics of Single Molecules in Short Distance Range with Subnanometer Sensitivity

Single molecule detection is useful for characterizing nanoscale objects such as biological macromolecules, nanoparticles and nanodevices with nanometer spatial resolution. Fluorescence resonance energy transfer (FRET) is widely used as a single-molecule assay to monitor intramolecular dynamics in the distance range of 3-8 nm. Here we demonstrate that self-quenching of two rhodamine derivatives can be used to detect small conformational dynamics corresponding to subnanometer distance changes in a FRET-insensitive short-range at the single molecule level. A ParM protein mutant labeled with two rhodamines works as a single molecule adenosine 5'-diphosphate (ADP) sensor that has 20 times brighter fluorescence signal in the ADP bound state than the unbound state. Single molecule time trajectories show discrete transitions between fluorescence on and off states that can be directly ascribed to ADP binding and dissociation events. The conformational changes observed with 20:1 contrast are only 0.5 nm in magnitude and are between crystallographic distances of 1.6 and 2.1 nm, demonstrating exquisite sensitivity to short distance scale changes. The systems also allowed us to gain information on the photophysics of self-quenching induced by rhodamine stacking: (1) photobleaching of either of the two rhodamines eliminates quenching of the other rhodamine fluorophore and (2) photobleaching from the highly quenched, stacked state is only 2-fold slower than from the unstacked state.

Long-Range and Local Structure in the Layered Oxide Li1.2Co0.4Mn0.4O2

The layered oxides being considered as intercalation compounds for lithium batteries display significant differences between the long-range crystal structure and local arrangements around individual atoms. These differences are important, because the local atomic environments affect Li-ion transport and, hence, the oxide’s rate capability, by determining activation barrier energies, by blocking or opening Li-diffusion pathways, etc. Traditional diffraction methods provide key information on the average crystal structure. However, no single experimental technique can unequivocally determine the average long-range crystal structure and the distribution of local environments over crystallographic distances while retaining atomic-scale resolution. Therefore, in this study, we have employed a combination of diffraction, microscopy, and spectroscopy techniques to investigate the long-range (∼1 μm) and local structure (≤1 nm) of Li1.2Co0.4Mn0.4O2, which is a model compound for layered oxides being considered for...

Synthesis and structure of dinuclear dimethylene- or 1,4-phenylene-linked bis(decamethyltitanoceneoxide) (Ti III) complexes

The singly tucked-in titanocene [Ti(η 5-C 5Me 5)(η 5:η 1-C 5Me 4CH 2)] ( 1) reacts smoothly with ethylene glycol or hydroquinone to give bis(titanoceneoxide) (Ti III) complexes [CH 2OTi(η 5-C 5Me 5) 2] 2 ( 2) and [(η 5-C 5Me 5) 2TiOC 6H 4OTi(η 5-C 5Me 5) 2] ( 3) containing dimethylene and 1,4-phenylene link, respectively. EPR spectra of 2 in 2-methyltetrahydrofuran glass and 3 in toluene glass revealed that the unpaired d 1 electrons are in interaction to form triplet state molecules. The Ti–Ti distance derived from the zero-field splittings D for the two conformations of 2 (7.42 Å and 7.66 Å) are in good agreement with the Ti–Ti distance of 7.2430(7) Å from the X-ray diffraction single-crystal analysis. For 3, however, the Ti–Ti distance derived from D (7.65 Å) is by 1.47 Å shorter than the crystallographic distance of 9.1230(8) Å that indicates an enhancement of the through-space dipole–dipole interaction due to the presence of a conjugated quinonide link.

Negative thermal expansion in CuCl: An extended x-ray absorption fine structure study

Extended x-ray absorption fine structure (EXAFS) has been measured from liquid helium to ambient temperature at the $\mathrm{Cu}\phantom{\rule{0.2em}{0ex}}K$ edge of copper chloride (CuCl) to investigate the local origin of negative thermal expansion. A quantitative analysis of the first coordination shell, performed by the cumulant method, reveals that the nearest-neighbor Cu-Cl interatomic distance undergoes a strong positive expansion, contrasting with the much weaker negative expansion of the crystallographic distance between average atomic positions below $100\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. The anisotropy of relative thermal vibrations, monitored by the ratio $\ensuremath{\gamma}$ between perpendicular and parallel mean square relative displacements, is considerably high, while the diffraction thermal factors are isotropic. The relative perpendicular vibrations measured by EXAFS are related to the tension mechanism and to the transverse acoustic modes, which are considered responsible for negative thermal expansion in zinc-blende structures.

Steps along the Path to Dihydrogen Activation at [FeFe] Hydrogenase Structural Models: Dependence of the Core Geometry on Electrocatalytic Proton Reduction

Differences in the rate of electrocatalytic proton reduction by Fe2(mu-PPh2)2(CO)6, DP, and the linked phosphido-bridged analogue Fe2(mu,mu-PPh(CH2)3PPh)(CO)6, 3P, suggest that dihydrogen elimination proceeds through a bridging hydride. The reaction path was examined using electrochemical, spectroscopic, and in silico studies where reduction of 3P gives a moderately stable monoanion [Kdisp(3P-) = 13] and a distorted dianion. The monomeric formulation of 3P- is supported by the form of the IR and EPR spectra. EXAFS analysis of solutions of 3P, 3P-, and 3P2- indicates a large increase in the Fe-Fe separation following reduction (from 2.63 to ca. 3.1-3.55 A). DFT calculations of the 3P, 3P-, 3P2- redox series satisfactorily reproduce the IR spectra in the nu(CO) region and the crystallographic (3P) and EXAFS-derived Fe-Fe distances. Digital simulation of the electrocatalytic response for proton reduction indicates a low rate of dihydrogen evolution from the two-electron, two-proton product of 3P (H23P), with more rapid dihydrogen evolution following further reduction of H23P. Because dihydrogen evolution is not observed upon formation of H2DP, dihydrogen evolution at the two-electron-reduced level does not involve protonation of a hydridic Fe-H ligand. The rates of dihydrogen elimination from H2DP, H23P, and H2Fe2(mu,mu-S(CH2)3S)(CO)6 (H23S) are related to the DFT-calculated H-H distances [H23S (1.880 A) < H23P (2.064 A) < H2DP (3.100 A)], and this suggests a common reaction path for the thiolato- and phosphido-bridged diiron carbonyl compounds.

Formation of oxo-bridged tetrairon(iii) complexes mediated by oxygen activation. Structure, spectroscopy, magnetism and electrochemistry

The reaction involving 2,6-diformyl-4-methylphenol, 1,3-diaminopropane, iron(II) perchlorate and sodium acetate in the ratio (2 : 2 : 2 : 3) in methanol produces the acetate-bridged macrocyclic diiron complex [FeII2L(μ-O2CCH3)(CH3OH)2](ClO4) (1). The direct reaction between the perchlorate salt of the macrocyclic ligand [LH4](ClO4)2 and iron(II) perchlorate in the presence of a mixture RCO2H and triethylamine also produces in solution the diiron complex [FeII2L(μ-O2CR)]+ (where R = H, CH3, C2H5, (CH3)3C and C6H5), which on exposure to air readily transforms to the corresponding oxo-bridged tetrairon(III) complex [{FeIII2L(μ-O2CR)}2(μ-O)2](ClO4)2 (2–6). The X-ray crystal structures of the acetate (3) and benzoate-bridged (6) complexes have been determined. Variable temperature (4–300 K) magnetic susceptibility measurements carried out for 3 and 6, have been analyzed in terms of molecular field approximation. The dominant antiferromagnetic exchange interaction (J) occurring through the oxo-bridged diiron(III) is −115 cm−1 for 3 and −109 cm−1 for 6, while the magnitude of spin exchange coupling occurring through the phenoxide bridges (J′) is −4 cm−1 for both 3 and 6. Complexes 2–6 exhibit identical proton NMR spectra in CD3CN, indicating that the capped carboxylate ligand gets detached from the metal centres. The Fe⋯H distances estimated from relaxation time (T1 and T2) measurements have been found to agree well with the crystallographic distances. Complexes 2–6 exhibit identical electrochemical behaviour and undergo reduction in three steps involving a first two-electron transfer reaction to [{FeIILFeIII}2(μ-O)2]2+, followed by two one-electron two-proton coupled reactions to [FeIILFeII]2+.

A study of the Nb3Ge system by Ge K-edge extended x-ray absorption finestructure and x-ray absorption near-edge structure spectroscopy

The local structure of Nb3Ge intermetallic superconductor has been studiedby Ge K-edge absorption spectroscopy. Extended x-ray absorption finestructure (EXAFS) experiments show two Ge–Nb distances. In additionto the crystallographic distance of ∼2.87 Å, there exists a second Ge–Nbdistance, shorter than the first by ∼0.2 Å, assigned to a phase with short-rangesymmetry related to local displacements in the Nb–Nb chains. The x-rayabsorption near-edge structure (XANES) spectrum has been simulated by fullmultiple-scattering calculations considering the local displacements determined bythe EXAFS analysis. The XANES spectrum has been well reproducedby considering a cluster of 99 atoms within a radius of about 7 Å fromthe central Ge atom and introducing determined local displacements.

Site-selective EXAFS in mixed-valence compounds using high-resolution fluorescence detection: a study of iron in Prussian Blue.

A quantitative analysis is presented for the site-selective Fe K-edge absorption spectra of Prussian Blue: Fe(4)[Fe(CN)(6)](3) x xH(2)O (x = 14-16). The site-selective spectra were recorded using high-resolution fluorescence detection of the K beta emission from a polycrystalline sample. The K beta fluorescence lines arising from the high-spin and low-spin sites are shifted in energy. Since the emission features partially overlap, fluorescence-detected absorption spectra using different emission energies represent different linear combinations of the pure high-spin and low-spin EXAFS. A numerical method was used to extract the individual site EXAFS spectra from the experimental data. The analysis yields a range of solutions. A unique solution can be obtained if homovalent model compounds are used to simulate the K beta fluorescence emission from the two Fe sites in Prussian Blue. EXAFS analysis of the range of spectra obtained in the numerical method yields almost identical interatomic distances for the different spectra while the Debye-Waller factors vary considerably. The distances obtained in the EXAFS fit correspond to the crystallographic distances.

Metal-metal interactions in weakly coupled mixed-valence E- and Z-diferrocenylethylene complexes.

To study metal-to-metal interactions in mixed-valence states of two weakly coupling ferrocenyl groups assembled in E or Z conformation on an ethylenic double bond, E-1,2-dimethyldiferrocenylethylene (1), Z-1,2-dimethyldi-ferrocenylethylene (2), and 1,2-diferrocenylcyclohexene (3) were synthesized and structurally characterized. Crystals of 1 are triclinic, P1, with a = 7.494(9) A, b = 10.801(3) A, c = 11.971(2) A, alpha = 102.17(2) degrees, beta = 106.12(9) degrees, gamma = 90.42(2) degrees, V = 907.8 A3, and Z = 2. Crystals of 2 are monoclinic, P2(1)/c, with a = 13.601(8) A, b = 11.104(4) A, c = 13.732(1) A, beta = 114.26(7) degrees, V = 1890.8(3) A3, and Z = 4. Crystals of 3 are orthorhombic, P2(1)2(1)2(1), with a = 5.766(2) A, b = 13.090(1) A, c = 26.695(2) A, V = 2014.9(3) A3, and Z = 4. Intervalence transition spectra (IT) and electrochemical data have been determined and compared with those of diferrocenyl-benzene (para, ortho, and meta). The comproportionation constants in nitrobenzene at 25 degrees C were found to be 490 and 813 for 1 and 3, respectively. That of 2 was not measured because of the fact that 2+ isomerizes rapidly in all solvents tested, yielding nearly a racemic mixture of E and Z conformers. This finding helps to clear the paradoxical phenomenon between experimental results of mixed-valence complexes of E- and Z-1,2-bis(1'-ethyl-1-ferrocenyl)-1,2-dimethylethylene and theories. The stability of the mixed-valence species was discussed in terms of resonance delocalization, Coulomb repulsion energy, inductive effect, magnetic interaction, structural factors, and statistical factor. According to our analysis based on the Hush formalism, the contribution due to Coulomb repulsion energy dominates the overall stability of the mixed-valence state in 1+, 2+, and 3+. Stabilization that arises from resonance delocalization is only minor and contributes less than 4% to the overall stability, even in 3+ where linked Cp rings and the ethylenic plane are coplanar. In calculating the resonance contribution, crystallographic Fe-Fe distances of 7.44 A (1) and 6.68 A (3) were used for 1+, and 3+, respectively.

15N NMR study of proton localization and proton transfer thermodynamics and kinetics in polycrystalline porphycene

Using high-resolution solid-state 15N cross-polarization magic angle spinning NMR techniques, the proton transfer thermodynamics and dynamics and the proton locations in polycrystalline 15N-labeled porphycene were studied. Whereas at room temperature only a single 15N resonance is observed, indicating an equivalence of all nitrogen atoms arising from a quasi-degenerate fast proton transfer, four signals are observed at low temperatures, exhibiting temperature-dependent line positions. Their analysis is consistent with the presence of either (i) two different molecules A and B in the asymmetric unit, each of which is subject to a quasi-degenerate correlated double proton transfer, or (ii) a single molecule exhibiting all four possible near-degenerate tautomeric states, two trans- and two cis-tautomers, interconverting by fast single proton transfers. The average rate constants of the proton transfer processes are found to be in the nanosecond time-scale. These constants were obtained between 228 and 355K by analysis of the longitudinal 9.12 MHz 15N T1 relaxation times, which exhibit a minimum around 280 K. The relaxation analysis was performed in terms of a quasi-degenerate two-state proton transfer process which modulates the heteronuclear 1H–15N dipole–dipole interaction. From the value of T1 in the minimum, the crystallographic NN distance of 2.63 A and the hydrogen bond correlation for N—H···N hydrogen bonded systems, the two N···H distances of 1.10 and 1.60 A were obtained, i.e. a hydrogen bond angle of 152°, which are significantly different from the corresponding values of 1.03 and 2.28 A and 116° found for porphyrin. The analysis of the temperature dependence of the rate constants indicates tunneling as a major reaction pathway, involving a barrier of about 32 kJ mol−1. The finding of a larger NH distance and a smaller barrier for proton transfer as compared with porphyrin is rationalized in terms of the stronger intramolecular hydrogen bonds in porphycene. A strong coupling between these bonds would indicate that the proton tautomerism in porphycene corresponds to a correlated double proton transfer, in contrast to the stepwise transfer in porphyrin. Finally, a relation between the intrinsic 15N chemical shifts of porphyrinoids and the N···H distance was found, which might be useful for estimating geometries of porphyrinoids. Copyright © 2000 John Wiley & Sons, Ltd.

Rotational resonance NMR of [formula omitted]-labelled retinal: quantitative internuclear distance determination

Rotational resonance phenomena are investigated in the solid-state magic-angle spinning NMR of all- E-[11,20- 13 C 2 ]-retinal at a magnetic field of 4.7 T. We find good agreement between experiments and numerical simulations for the rotational resonance spectral peakshapes and for the rotor-driven magnetization exchange. The internuclear distance between the 13 C -labelled C11 and C20 sites is determined to be 0.301±0.008 nm (from rotational resonance spectra) and 0.300±0.010 nm (from rotor-driven magnetization exchange), in agreement with the X-ray crystallographic distance of 0.296 nm. We show rotational resonance spectra which display perturbations from intermolecular homonuclear spin–spin interactions.

Growth of Highly Ordered Thin Silicate Films at the Air−Water Interface

The growth of thin silicate−organic films at the air−water interface of surfactant solutions has been studied in situ by X-ray and neutron reflectivity to a resolution of ca. 5 Å. Surfactant in the solution and the air−water interface itself are involved in directing the growth and final structure of the films. Hexadecyltrimethylammonium chloride (C16TAC) and bromide (C16TAB) have been used as the templating surfactants, and the film structure is independent of the anions under the conditions used. In situ X-ray and neutron reflectivity measurements at an early stage of film growth show a slow development of structure in the top 100 Å of the solution, which is consistent with a monolayer of tilted surfactant molecules at the air−water interface, a layer of partly silicated material, and an interdigitated surfactant bilayer or layer of cylindrical micelles oriented with their long axes parallel to the surface. Following this induction period a rapid crystallization occurs to give a structure with a crystallographic repeat distance of 45 Å perpendicular to the surface and composed of alternating surfactant layers and silicate material. The very narrow observed diffraction peaks indicate that the final silicate film is highly ordered.

Two modes of ligand binding in maltose-binding protein of Escherichia coli. Electron paramagnetic resonance study of ligand-induced global conformational changes by site-directed spin labeling.

Binding of ligands to the maltose-binding protein (MBP) of Escherichia coli often causes a global conformational change involving the closure of its two lobes. We have introduced a cysteine residue onto each of these lobes by site-directed mutagenesis and modified these residues with spin labels. Using EPR spectroscopy, we examined the changes, caused by the ligand binding, in distance between the two spin labels, hence between the two lobes. The binding of both maltose and maltotetraose induced a considerable closure of the N- and C-terminal lobes of MBP. Little closure occurred upon the binding of maltotetraitol or beta-cyclodextrin. Previous study by fluorescence and UV differential absorbance spectroscopy (Hall, J. A., Gehring, K., and Nikaido, H. (1997) J. Biol. Chem. 272, 17605-17609) showed that maltose and a large portion of maltotetraose bound to MBP via one mode (R mode or "end-on" mode), which is physiologically active and leads to the subsequent transport of the ligands across the cytoplasmic membrane. In contrast, maltotetraitol and beta-cyclodextrin bound to MBP via a different mode (B mode or "middle" mode), which is physiologically inactive. The present work suggests that the B mode is nonproductive because ligands binding in this manner prevent the closure of the two domains of MBP, and, as a result, the resulting ligand-MBP complex is incapable of interacting properly with the inner membrane-associated transporter complex.

The crystalline structure of poly(3-octylthiophene) at high pressure

The crystalline structure of poly(3-octylthiophene) as a function of pressure up to 3 GPa (30 kbar) has been studied by energy dispersive x-ray diffraction. The distance between neighbouring thiophene chains in the direction normal to the thiophene rings, bperpendicular to , has been found to decrease with increasing pressure. This is believed to increase the planarity of the polymer main chains and explains why the thermochromic transition is inhibited under pressure. The crystallographic repetition distance a in the direction along the octyl side chains is found to be constant during increment of pressure. This shows how the alkyl side chains in cooperation act as rigid interchain spacers even if, independently, they are flexible and rather disordered. A lack of change in the interchain charge complex transfer integral can be understood from the pressure behaviour of a. The measurements indicate that the crystalline fraction of this paracrystalline polymer increases with pressure, and that the size of the crystalline domains increases slightly.

Bond distances in octahedral [SnCl 5L] − complexes by Mössbauer spectroscopy

The relationship between the Mössbauer partial quadrupole spliting (pqs) of the ligands and the crystallographic Sn-Cl distances, has been studied for [SnCl 5L] − complexes. While the Sn-Cl distance trans to L is not very sensitive to the nature of the ligand, the Sn-Cl distances cis to L and the average Sn-Cl distance decrease linearly for increasing values of pqs(L). The slopes of the plots d(Sn-Cl) vs 4pqs for SnCl 4L 2 and [SnCl 5L] − complexes, are in the ratio 2.6(3):1, in good agreement with the ratio 2.5:1 expected on the basis that in SnCl 4L 2 there are 2 L groups for 4 Cl atoms, while in [SnCl 5L] − there is only one L group for 5 Cl atoms. For the isoelectronic SbCl 5L complexes, the Sb-Cl bond distances are also linearly related to the 121-Sb quadrupole coupling constants. Therefore, both 121-Sb Mössbauer and NQR spectra can be used to predict Sb-Cl distances.

Bond valence sum analysis of metal-ligand bond lengths in metalloenzymes and model complexes

Bond valence sums (BVS's) have been calculated for a series of model complexes for important metalloenzymes. Values calculated from crystallographic distances predict the correct oxidation state of the metal center in a wide range of structural types. Many of the selected complexes have previously been studied by X-ray absorption spectroscopy, and first-shell metal-ligand bond distances have been determined by analysis of extended X-ray absorption fine structure (EXAFS)

Model-independent refinement of interproton distances generated from 1H NMR overhauser intensities

A recursive method to refine interproton distances compatible with two-dimensional nuclear Overhauser effect (NOESY) experiments has been tested. Convergence does not depend on the initial estimate of the parameters. Hence, no approximate initial structure of the molecule is required: the iterative process can be started from the experimentally measured NOESY cross-peak volumes, supplemented with arbitrary cross-peak and autopeak values to obtain an initial NOESY matrix. The relaxation matrix is calculated from the NOESY matrix, and its diagonal elements ( ϱ i ) are adjusted at each iteration until the difference between theoretical and experimental cross peaks is a minimum. The improvement comes from using interproton distances calculated from the off-diagonal ( σ ij ) elements to generate ϱ i values. The method was applied to alumichrome, a rigid cyclohexapeptide of virtually identical solution and crystallographic structures. The experimental data consisted of the integrated volumes of NOESY cross peaks at 500 MHz. Convergence was tested by resorting to different initial conditions, one of them being a NOESY matrix in which the experimentally unobserved off diagonal elements were set equal to zero and the diagonal elements to 0.5. The iterations rapidly converge, in all cases, to a set of distances whose root-mean-squares deviation (rmsd) from the crystallographic distances is < 0.05 Å. The acronym MIDGE (model-independent distance generation) for the procedure is proposed.