Their IR features are hardly distinguishable at finite temperature. The major difference concerns the mode of spin coupling between the terminal beryllium and carbon atoms. Further, the ground‐state potential‐energy surface of the  system at 4 K is presented and differences between the photochemical and thermal behaviors are highlighted. Finally, a previously not considered, so far unknown Cv2‐symmetric rhombus‐like four‐membered ring 3[Be(O)(C)Be] (35) is predicted to represent the global minimum on the potential‐energy surface.Extensive high‐level quantum‐chemical calculations reveal that the rod‐shaped molecule BeOBeC, which was recently generated in matrix experiments, exists in two nearly isoenergetic states, the  One way or another: The coexistence of two isoenergetic electromers of the novel BeOBeC molecule, possessing practically indistinguishable IR features, has been revealed by quantum‐chemical calculations. Further, the triplet state of a so far unknown Cv2‐symmetric rhombus‐like four‐membered ring 3[Be(O)(C)Be] is predicted to represent the global minimum on the potential‐energy surface in the thermal reaction of Be2 with CO. The simplest carbyne, methylidyne (HC), was one of the first molecules to be identified as a constituent of interstellar space.2CO complex, upon exposure to visible light, rearranges to the insertion intermediate Be(CO)Be; the latter isomerizes further under UV irradiation to BeOBeC (Scheme 5Σ state with an electronic configuration (α)BeOBeC(ααα), where the unpaired electrons at the terminal Be and C atoms are ferromagnetically coupled, was assigned as the ground state among all isomers considered. A triplet 3Π state with an (α)BeOBeC(αβα) electronic configuration, involving a doublet carbyne moiety, was calculated to be significantly less stable (>80 kJ mol−1) than the 5Σ state.2CO to BeOBeC and other conceivable isomers, were not reported.For simple carbyne radicals, both experiment and theory indicate that the reactivities of the doublet and quartet states of these molecules differ, and the electronic ground state most often corresponds to the doublet state;C Scheme . The proInterest in carbyne‐related species and particularly in the often decisive role of spin states5Σ (56), or should the co‐existence of other spin states, for example, the triplet 36 (3Σ), also be considered?Which multiplicity and which electronic configuration of BeOBeC actually correspond to the most stable electromer? Is the assignment of only one electronic state2 with CO look like? Are there other, perhaps more stable  isomers?How does the potential‐energy surface (PES) for the thermal reactions of Be2—a seemingly simple molecule having only eight electrons—still poses an enormous challenge for its correct quantum‐chemical description. In fact, the Be2 case was considered “pathological”.2 had already been published by 2009.1Σg+ of Be2,A proper theoretical description of beryllium‐containing molecules is all but trivial. Even the beryllium dimer Be5Σ state revealed a good agreement.3Σ species (36) in which the unpaired electron at the terminal beryllium atom is antiferromagnetically coupled to one of the unpaired electrons at the carbon unit, was not discussed in the previous publication.A comparison of the experimentally obtained with the calculated IR spectrum of the linear BeOBeC isomer in its 3,56) are almost isoenergetic at 4 K, with a tiny energetic preference for 56. We note that state‐specific CASSCF calculations indicate that 36 features significant multireference character .+ and Mg2O2+.6 prefers a triplet ground state; for details, see Table S2.As shown in Table 36 and 56 are practically indistinguishable (see Tables S3 and S4), an experimental differentiation and unambiguous assignment of these ferro‐ and antiferromagnetically coupled states would require an approach based on the different magnetic properties of the two multiplicities. In the absence of these data, a definitive assignment on the actual electronic configurations and spin states of BeOBeC (6), generated according to Scheme Since the IR spectroscopic features of 3,56 points to another unexpected facet. The spin distributions of 3,56, given in Table 6 we note quite some delocalization of the spin as illustrated in Figure 3,56 calculated at the CASSCF level are the same.Quite interestingly, a more detailed inspection of the spin density of the individual atoms of 6) was generated at 4 K by light‐induced isomerization of Be2CO 3,56, in addition to being almost isoenergetic, exhibit both practically identical geometric features . Obviously, under thermal conditions the generation of 35 would clearly dominate the whole scenario. 35 is predicted to have six vibrational fundamentals, all have appreciable IR intensities . However, there is no experimental evidence in forming this isomer in the light‐induced reaction of Be2 with CO in solid neon.−1 could appear to be assigned to 5 (Tables S3 and S4), the isotopic shifts obtained by 18O and 13C labelling rule out this assignment; rather, they are only compatible with linear Be(CO)Be (7).As shown in Figure 6), the actual multiplicity has yet to be determined, as both the almost isoenergetic quintet and triplet states of 6 cannot be distinguished unambiguously by the currently available methods. Most likely, these two differently spin‐coupled electronic states co‐exist at finite temperature. Not surprisingly, the pathways in the thermochemical and photochemical transformations of  differ, although some of the products, for example, 6 and 7, are accessible on either route. While the global minimum Be(O)(C)Be (5) cannot be formed photochemically,2/CO couple to create this hitherto unknown rhombus‐like four‐membered ring.In conclusion, in this computational study, novel insight is provided into the features of some  isomers. Quite importantly, for the IR‐spectroscopically identified isomer BeOBeC  should be addressed to the authors.SupplementaryClick here for additional data file.


Analysis of the X-ray beam-induced dynamics in oxide glasses probed by X-ray photon correlation spectroscopy is presented. The results offer the possibility to estimate true sample relaxation time by performing two measurements with different X-ray fluxes. 2, GeO2 and B2O3 glasses, it is concluded that the beam-induced dynamics show rich behavior depending on the sample.Probing the microscopic slow structural relaxation in oxide glasses by X-ray photon correlation spectroscopy (XPCS) revealed faster than expected dynamics induced by the X-ray illumination. The fast beam-induced dynamics mask true slow structural relaxation in glasses and challenges application of XPCS to probe the atomic dynamics in oxide glasses. Here an approach that allows estimation of the true relaxation time of the sample in the presence of beam-induced dynamics is presented. The method requires two measurements either with different X-ray beam intensities or at different temperatures. Using numerical simulations it is shown that the slowest estimated true relaxation time is limited by the accuracy of the measured relaxation times of the sample. By analyzing the reported microscopic dynamics in SiO Glasses are amorphous solids and their structural relaxation is too slow to be observed at the laboratory time scale. At Tg the shear viscosity of a liquid η is 1012 Pa s and the structural relaxation time τ is 100 s by convention. According to Angell  shows a rich behavior that reflects the dramatic slowing down of the molecular motions  has been developed as a powerful tool to probe the structural relaxation time at the atomic length scale  or linked boroxol groups randomly arranged in a three-dimensional network  autocorrelation function, t0 and q is the magnitude of the scattering vector. g(2) is related to the intermediate scattering function f = S/S(q) via the Siegert relation g(2) = 1 + C[f]2, and C is a contrast that depends on the experimental setup and sample properties. The intermediate scattering function describes the relaxation process in space and time, et al., 2012et al., 2017q and the temperature T. For ‘strong’ glass-formers the temperature dependence of the sample relaxation time τs(T) can be described by the Arrhenius behavior 0 is a constant, Ea is an activation energy and kB is the Boltzmann constant.The measured quantity in XPCS is a temporal intensity F, the measured relaxation time τ is composed of two contributions: the intrinsic dynamics of the sample τs(T) and the beam-induced dynamics τind(F),et al.  at different F, we can fit it with a simple linear model y = b + ax. Then the intercept b provides an estimate of the relaxation rate of the sample 1/τs(T). This is the basic principle used in the proposed approach but its application is not trivial as we shall see below.Then equation (1)s(Tlow) ≫ τind(F) and we can assume that the measured relaxation time is dominated by the beam-induced effect: τ = τind(F). Conversely, at high temperatures, above Tg, F, Thigh) = τs(Thigh). From the above asymptotic behavior we can envisage measuring the relaxation time at low temperature and use τind(F) = τ for estimating the sample dynamics in the intermediate range near Tg using ind(F) = τ. Assuming that τind(F) is temperature independent we can estimate it by measuring the dynamics at low temperature and then use this value to estimate the sample dynamics around Tg. For SiO2, GeO2 and B2O3, room temperature can be considered as low enough.Based on the above principle we can consider two practical cases. The first: at low temperatures, in the deep glassy state, τind might not be valid then we can exploit the fact that the beam-induced effect is a linear function of the flux F, and by performing measurements using only two different fluxes one can estimate the true sample relaxation time. To accomplish the estimation we must know the ratio f = F1/F2  between two different fluxes used, then it is easy to show that the sample relaxation time can be obtained byThe second case: when the temperature independence of τ3.F, T). The temperature dependence of the sample relaxation time τs(T) was described by the Arrhenius equation using parameters for Ea of B2O3 glass  = 100 s (Tg = 580 K)  to 20 s. Using equation (1)F, T) adding the noise  with Gaussian noise σ of 1% we obtained an estimation of τs(T) displayed by the gray circles in Fig. 1To study the effect of noise on the estimation of the sample relaxation time we performed numerical simulations. We modeled the experimental noise using a Gaussian distribution with a relative standard deviation σ = 1% of the mean value for τ(ind(F) and τ. At low temperatures τ asymptotically approaches τind and σs diverges. Adopting a 3σ criterion that τind − τ ≥ 3σ[τind + τ] and setting τind − τ = 6στ into equation (4)The flattening results from the behavior of the relative variance F1, T) and τ, both with σ = 1%. At high temperatures gray points are narrowly distributed and coincide with the theoretical value (blue line). At low temperatures we observe a wide distribution of the estimated relaxation time and it deviates from the expected behavior (blue line). The blue squares are average values. At low temperatures the average values deviate from the expected time and saturate at a certain level. The black dash-dot line is the upper limit. The relative variance fτ − τ ≥ 3σ[fτ + τ] and setting fτ − τ = 6σfτ into equation (5)Now we consider the second case when two measurements with different fluxes are performed at constant temperature. Such a case has an advantage because it can be applied when the beam-induced dynamics might be temperature dependent. The simulated curves (red and dashed green) are shown in Figs. 2ind or τ when it is measured with an accuracy of 1%}. In the near future, 100 times higher coherent flux is expected from the new diffraction-limited synchrotron sources  of the correlation function g(2) according to the following equation  but the absolute values will decrease by a factor of 100. The calculation of this scenario is shown in Fig. 3F2, T) = 200 s with σ = 1% and set f = 100 and τ = 2 s with σ = 0.1%. As one can see, the behavior is qualitatively identical to the previous case but the deviation from the sample relaxation time occurs at a factor of two slower times. Thus, it is possible to estimate the sample time to be 30 times slower than τ. This example shows that it is feasible to take advantage of the increase in coherent flux. To obtain the most optimal estimation of the true sample relaxation time within the available measurement time tacq one should use the same time tacq for both measurements and seek to work with the smallest σ; and f should be larger than 15.These results show that, in practice, the sample relaxation time can be estimated reliably up to a certain time {approximately 16.6[1/(6 × 0.01)] times slower than τ4.et al., 2017et al., 2019et al., 2015et al., 2015et al., 2009et al., 2010et al., 2013The analysis performed in this study relies on the decoupling of the beam-induced relaxation time from the true sample relaxation time and its strong temperature dependence. It retrieves the sample dynamics without knowing the origin of the beam-induced effect. However, studying both dynamics is important for a better understanding of the glass transition problem and for application of oxide glasses in radiation-high industrial environments. This study addressed the first problem, and the latter one requires further investigation. Recent works q2. This allows us to compare beam-induced microscopic dynamics with the well understood diffusion process in a colloidal suspension where particles randomly move in a viscous liquid. For a dilute colloidal suspension undergoing Brownian motion the reduced relaxation time is inversely proportional to the diffusion coefficient D, τ(q)q2 = 1/D , τ(q)q2 ∝ S(q)/D q2 = c + kq, where c and k are constants. The constant k depends on the incident X-ray flux while the parameter c is negative and similar for all three curves. The linear behavior and compressed shape of the exponential decay 30(B2O3)70 glass (Holzweber et al., 20192O3 glass transforms trigonal BO3/2 into tetragonal Clearly, in multicomponent oxide glasses the real picture can be more complex. A new study of alkali borate glasses reported a deviation from the single linear behavior in (Rb5.Tg. The observation of diffusive and superdiffusive microscopic behaviors of the beam-induced dynamics and deviation from the linear dependence on the incident flux in various oxide glasses calls for further studies.The measurements of microscopic dynamics in oxide glasses by XPCS are inevitably affected by the beam-induced structural rearrangements that preclude determination of the true sample structural relaxation time at the atomic length scale. However, when beam-induced atomic motion is a linear function of the X-ray flux, then, by performing two measurements, either at two different temperatures or with two different fluxes, it is possible to estimate the true sample relaxation time in simple glasses up to a certain extent into the glassy state. This extent depends on the accuracy of the measured relaxation times. Therefore, the application of XPCS for the investigation of atomic dynamics in oxide glasses will largely benefit from the increase in precision of measuring the intermediate scattering function, and determination of the relaxation time and the shape parameter. Moreover, the described framework can be useful for developing a better understanding of non-linear beam-induced effects and many intriguing properties of oxide glasses and supercooled liquids around


SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy‐number by next‐generation sequencing (NGS) very difficult. Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy‐number using NGS data. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify silent carriers. This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes Project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation. This combination makes it especially suitable to be integrated into production NGS pipelines. Source code and documentation are available at https://www.github.com/babelomics/SMAca.Spinal muscular atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of  A total of 95%–98% of SMA patients show a complete absence of at least exon 7 of SMN1. Most of the remaining patients have a single copy of the SMN1 gene which is inactive due to point mutations or deletion of exons 1–6. The disease severity is determined mainly by a copy gene, SMN2. The more SMN2 copies present, the milder the phenotype usually is. Both genes, located on chromosome 5q13.2, can be distinguished by only five nucleotides  is an autosomal recessive disorder caused by degeneration of alpha motor neurons in the anterior horn of the spinal cord, leading to hypotonia, muscular atrophy, and weakness of proximal muscles, predominantly affecting the lower extremities, being respiratory insufficiency a frequent cause of death in the most severe cases  known as “silent carriers”  or 0.5 (2:0) and, in both cases, the scaled coverage proportion of SMN1 should be close to ½ in each position. Finally, a variant, referred to as SMN1/2∆7‐8, contains one or two extra copies of SMN exons 1–6 of SMN1 or SMN2. This variant is often present in individuals with no, or only one, SMN2. Although it is frequently found (23%) in Spanish carriers and noncarriers, its clinical significance is not yet completely understood  nor subtle mutations in SMN1 . However, next‐generation sequencing (NGS) technology is rapidly becoming a cost‐effective approach for clinical testing  of SMN1 copy‐number from NGS data. Moreover, SMAca can exploit the knowledge variants specific to SMN1 duplication to identify the silent carriers, following the recommendations for SMA carrier testing by the American College of Medical Genetics and Genomics . Finally, the whole set of BAM files were analyzed with SMAca in a single batch.The data were generated in the CNAG  with a NovaSeq 6000, using paired‐end reads (2 × 150 bp). Raw FASTQ files were processed following a standard NGS pipeline. Briefly, after filtering out low quality reads with https://www.internationalgenome.org/data-portal/sample; 1000 Genomes Project Consortium, SMN1 and SMN2 validated copy number statuses were obtained from Vijzelaar et al.  for each sample /Hki, were ci1 and ci2 are the average coverage for the whole genes SMN1 and SMN2, and Hki is the average coverage for the control gene k in the ith sample. Then, the scale factor θˆi=(∑k=1KZki/Z¯k)/K, where Z¯k=(∑i=1NZki)/N, N is the total number of samples and K the total number of control genes, is calculated for each sample. Finally, the raw proportion of SMN1 reads are scaled: πij=θˆi×D1ij/(D1ij+D2ij), where D1ij and D2ij are the raw coverage for SMN1 and SMN2 at position j in the ith sample.In particular, the relative coverage of 2.3SMN1 (πij) less than ⅓ in positions a, b, or c were marked as likely carriers. The scale factor θˆi  and the raw proportion of SMN1/SMN2 depth of coverage at positions a, b, and c (D1ij/D2ij), were used to estimate the absolute copy‐number as follows:SMN1:3 SMN2 are expected to have θˆi ∼ 1 and D1ij/D2ij ∼ ⅓.Genotypes 1 SMN1:2 SMN2 are expected to have θˆi ∼ 0.75 and D1ij/D2ij ∼ ½.Genotypes 1 SMN1:1 SMN2 are expected to have θˆi ∼ 0.5 and D1ij/D2ij ∼ 1.And genotypes 1 Results were classified following some simple rules. Samples with a scaled coverage proportion of SMN1  or 0.5 (2:0) and, in both cases, the scaled coverage proportion of SMN1 should be close to ½ in each position.To detect silent carriers, we select samples with two polymorphisms (g.27134T>G and g.27706_27707delAT) associated with duplication events in Therefore, SMA carriers can be detected either in genome or exome sequences, and even small panels as long as SMN locus and control genes are covered. However, for silent carriers, which require the analysis of some intronic positions, the use of genomic sequences is recommended.33.1SMN1/2∆7‐8).To test the reliability of SMAca predictions in a real scenario, we leveraged our participation in the Navarra 1000 Genomes Project NAGEN1000 to screen a dataset of 326 genomes. Among them, seven samples (2.15%) were identified as putative SMA carriers and successfully validated by MLPA (Table S1a–d). Interestingly, the percentage of the predicted and further confirmed SMA carriers in our dataset fits perfectly to the expected carrier frequency (2.10%) previously described in the bibliography  and an F1 score (Jackson et al., 3.2With the idea of facilitating the introduction of SMAca in production NGS pipelines, it has been optimized for running in different computer environments. Special stress has been made in the parallelization for exploiting multiple cores/processors when available. Figure 4SMN1 copy‐number from NGS data. As a conceptual novelty, SMAca includes the analysis of two polymorphisms that have been linked to silent carriers (Luo et al., SMN1 + SMN2, the results must be consistent across different populations given that the total SMN copy number tends to be constant (Vijzelaar et al., Here, we present SMAca, the first freely available python tool to detect SMA carriers and estimate the absolute The authors declare that there are no conflict of interests.Supporting information.Click here for additional data file.Supporting information.Click here for additional data file.


The series includes a rare new example of a tridentate T‐shaped AgI complex. Post‐complexation modification of the AuI complex provides access to a linear cationic AuI complex following ligand alkylation, or the first example of a cationic square planar AuIII−F complex from electrophilic attack on the metal centre. Emissions ranging from blue (CuI) to orange (AgI) are obtained, with variable contributions of thermally‐dependent fluorescence and phosphorescence to the observed photoluminescence. Green emissions are observed for all three gold complexes . The higher quantum yield and longer decay lifetime of the linear gold(I) complex are indicative of increased phosphorescence contribution.The photophysical properties of a series of T‐shaped coinage  T‐Shaped coinage‐metal complexes: Photoluminescence tuning mediated by a bis(mesoionic carbene)amido pincer ligand for d10 complexes of unusual T‐shape, linear AuI and square planar AuIII. One of the more successful design strategies on this front employs the linear bonding geometry of carbene‐metal‐amides (CMAs), in which all three d10 metals , have similarly accomplished excellent EQE performance and/or high brightness OLED operation, notably employing carbazolide derivatives as the donor amide partners with the acceptor carbenes.In the development of efficient organic light emitting devices (OLEDs), basic requirements of phosphorescent emitters include high external quantum efficiencies (EQE) of the emission, coupled with appropriate radiative lifetimes in the order of microseconds to facilitate the intersystem crossing (ISC) from the triplet to the singlet state.d10 coinage metal complexes is well‐known,3CNC]PF6⋅Cl, Figure I (1)I (3)I  enabled by both the strained T‐shape geometry and the strongly electron donating nature of the ligand, could be exploited for reactions with electrophiles at either the nucleophilic carbazolide amido AuI]+ or oxidized [(CNC)AuIIIR]+  complexes, respectively.d10 coinage metals and square planar cyclometallated gold(III) complexes, we decided to expand the series of complexes to include also AgI , as well as the appearance of the carbene carbon atom doublet of doublets  in the 13C NMR spectrum , confirm the formation of 2. A T‐shape geometry is unambiguously shown in the molecular structure obtained for a single crystal of 2 . A single two‐electron oxidation event was observed. Remarkably, the potential for the AuI/III couple was determined to be E0=−0.39 V, and at least quasi‐reversible with paE−Epc=97 mV to confirm viability of mild chemical oxidation, in line with quantum theoretical studies.5 was prepared by in situ deprotonation of [H3CNC]PF6⋅Cl and metalation to yield, after purification and isolation, complex 3 (Scheme 3 with a stoichiometric amount of the fluorinating agent Selectfluor in THF yielded 5 (37 % yield) .The facile chemical oxidation of complex 5 was isolated as a lime‐green solid and is the first example of a stable, monomeric cationic gold(III) fluoride. The disappearance of the gold(I) carbene carbon resonance of 3 (δC 176.0 ppm) is consistent with an AuI/III oxidation event, although the expected upfield shifted AuIII carbene carbon atom resonance was not detected. The 19F NMR spectrum displays fluorine resonances at δF −299.9 and −153.2 ppm, respectively, for the Au−F− and BF4− counterion. The fluoride resonance of −299.9 ppm is significantly upfield from neutral gold(III) fluorides (δF −255 ppm),Well‐defined, isolable gold(III) fluorido complexes are not common, although they have been implicated as transient catalytic intermediates.5 , with the first singlet S1 resting above, but close to T1, which is compatible with an efficient S1–T1 ISC (ISC = intersystem crossing).1 states are mainly located on the M−N bond, regardless of the nature of the transition metal. The lowest contribution of the metal is found for CuI, in agreement with the significantly lower extinction coefficient found for 1, compared to 2 and 3.In all cases, the TD‐DFT calculations indicate that the most stable excited state of the complexes is a triplet →π*(carbene)] 3ILCT excited state.The emission band of the ligand precursor in THF at 298 K is broad and featureless, which is typical of emissions of [π(carbazole)→π*(triazolium)] ILCT origin. The emission spectra recorded for complexes 4 is red‐shifted when compared to the ligand precursor, owing to the coordination of AuI metal centre to the carbene moieties. On the other hand, complex 5 showed a vibronic emission band, which is tentatively assigned as originating from an intraligand (3IL) excited state, probably arising from the higher oxidation state of the AuIII centre that reduces the ease of donation from the carbazolide, leading to a higher‐lying 3ILCT state. For complex 3, vibronic‐structured 3IL emission is observed in THF, whereas structureless 3ILCT emission is found in acetonitrile, showing that the 3ILCT and 3IL excited states are close in energy, and their energies are affected by solvent polarity. The observation of the structureless emission can be attributed to the stabilization of the 3ILCT state by the polar acetonitrile, which leads to the 3ILCT state becoming the lowest energy excited state responsible for emission. In glass matrices at 77 K, the complexes in general showed vibronic emission bands, originating from the 3IL excited state, probably due to the destabilization of the 3ILCT state in glass matrices. The photoluminescence quantum yields of the compounds are low, ranging from 0.6 % for 3 (T‐shaped AuI) to 14 % for 4 (linear AuI). The emission wavelengths range over 180 nm (≈6100 cm−1) with the use of different metals for color‐tuning in the T‐shaped complexes1 CuIλem=460; 3 AuIλem=510–652 nm; 2 AgIλem=640 nm), and the copper(I) complex displaying uncommon blue emission.The emission of the two‐coordinated complex 1 is too short to be determined with certainty in THF at 298 K, and the emission may be fluorescent in nature.2–4, the decay lifetimes are in the microsecond range for 2 (τ0=0.4 μs), 3 (τ0=0.4 μs) at room temperature, but increase to τ0=4.75 ms and 2.41 ms, respectively, upon cooling to 77 K in butyronitrile glass. The increase in excited state lifetime is in line with the assignment of a change in emission origin from predominantly 3ILCT to 3IL excited state, the latter of which typically shows longer lifetime. Such increase in τ0 at lower temperatures by four orders of magnitude may also suggest the occurrence of TADF, with thermal population of S1 allowed due to fast reversible or equilibrium ISC (rISC) if ΔE(T1−S1) <0.37 eV .E(T1−S1) leads to lower radiative rates and ΦPL.The luminescence lifetimes of the complexes were measured at 298 K and 77 K. The lifetime of complex 3–5, the calculated energy transitions (both ΔE(T1−S0) and ΔE(T1−S1) (Table S2)), match that of the experimental emission energies, with 3<5<4 (Table S2). In this case, all three gold complexes have green emissions. For the linear AuI complex 4, ΔE(T1−S1)=0.419 eV, which is prohibitive for rISC (T1→S1) and should suppress TADF. Greater phosphorescence contribution to the photoluminescence leads to longer decay times in THF at 298 K . A significantly lesser increase in decay time for 4 upon cooling to 77 K in butyronitrile glass , together with the highest ΦPL observed for 4, supports such increased phosphorescence contribution. In conclusion, the bis(mesoionic carbene)carbazolide CNC pincer ligand allows for modulation of the photophysical properties of complexes, either with the introduction of different metals to access emissions from the blue to orange spectrum , or by modification of the complex with electrophilic attack at either the carbazolide‐N (4) or at the nucleophilic metal centre (5).Comparing the gold complexes 3CNC]PF6⋅Cl[H and complexes 1,342 and 5 are given in the Supporting Information for this paper. The molecular structures of 2 and 5 were determined by single crystal X‐ray crystallography.The precursor The authors declare no conflict of interest.As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re‐organized for online delivery, but are not copy‐edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.SupplementaryClick here for additional data file.


The acid stability of 1 was found to be greater than that of the analogous tetrahedron 2 built from 2‐formylpyridine. Intriguingly, the peripheral presence of additional pyridine rings in 1 resulted in distinct guest binding behavior from that of 2, affecting guest scope as well as binding affinities. The different stabilities and guest affinities of capsules 1 and 2 enabled the design of systems whereby different cargoes could be moved between cages using acid and base as chemical stimuli.The use of di(2‐pyridyl)ketone in subcomponent self‐assembly is introduced. When combined with a flexible triamine and zinc bis(trifluoromethanesulfonyl)imide, this ketone formed a new Zn A strategy for improving the acid resistance of a tetrahedral cage has been developed by incorporating additional free pyridyl units on its vertices. The guest binding properties of the cage are also altered compared to the analogous tetrahedron without these peripheral groups, allowing the functions of complete cargo delivery and exchange between the two capsules by using acid and base as chemical stimuli. Metal–organic cagesThe reversible nature of their coordination bonds1 ketone might be employed in place of 2‐formylpyridine during the construction of cages by subcomponent self‐assembly.A2N−, 4 equiv) and di(2‐pyridyl)ketone (12 equiv) or 2‐formylpyridine (12 equiv) in acetonitrile afforded tetrahedra 1 and 2 ketone 2 equiv ol)ketone 2 equiv ol)ketone 2 equiv o1 in the presence of other anions, including BF4−, TfO−, ReO4−, PF6−, and SbF6−, allowed us to obtain crystals of the anion adducts X−⊂1 suitable for X‐ray diffraction studies . In each case an anion is observed inside the cavity of 1, with the cavity volume expanding from 134 Å3 in [BF4−⊂1] to 148 Å3 in [TfO−⊂1] .Slow vapor diffusion of diethyl ether into acetonitrile solutions of s Figure  a–e.16 I6−⊂2] .The crystal structure of SbF6−⊂ . The smallest anion investigated, BF4−, bound within 1 (Ka=2.2×103 m−1), whereas no interaction was observed with cage 2. Cage 1 also bound all other anions (Ka=106–107 m−1) more strongly than 2 (Ka=104–105 m−1) . In contrast, cage 2 encapsulated neutral guests . Neutral guests containing five‐ and six‐membered rings were bound by both tetrahedra 1 (Ka=5–15 m−1) and 2 (Ka=91–680 m−1), whereas larger guests were observed to bind only within 2 (Ka <11 m−1). We infer that the restricted rotation of the phenylenes on the faces of 1, as noted above, prevented its cavity from adapting to bind the larger neutral guests, while the higher rigidity of 1 enhanced its ability to encapsulate the smaller anionic guests.The peripheral differences in the structures of 2) to a CD3CN solution of tetrahedron 2 led to the progressive disappearance of the cage peaks along with the appearance of new signals corresponding to free 2‐formylpyridine , indicating the disassembly of cage 2 upon acid addition. Complete disassembly of 2 was observed following the addition of 10 equivalents of HNTf2. In contrast, 30 equivalents of acid were required to induce complete disassembly of cage 1, with 43 % cage opening observed at 10 equivalents , indicating that 1 is more acid‐resistant than 2. Titration of the base N,N‐diisopropylethylamine  into the solution of disassembled 2 led to the progressive reformation of the cage, whereas no such regeneration was observed even after the addition of 30 equiv of DIPEA to disassembled 1 . The salts that build up following the addition of 30 equivalents each of acid and base may thus prevent the reformation of 1.Addition of hydrogen bis(trifluoromethanesulfonyl)imide  to an equimolar mixture of 1 and 2 in CD3CN led to the selective and complete disassembly of 2, with the 1H NMR signals for 1 remaining intact . This result further indicates the intrinsically higher stability of 1 towards acid, highlighting the utility of di(2‐pyridyl)ketone in subcomponent self‐assembly. Subsequent addition of DIPEA induced cage 2 to reform , regenerating the initial equimolar mixture of the two cages.The addition of HNTf1 and SbF6−⊂2, prepared separately and then mixed together. As triflimidic acid was progressively added to the mixture (up to 9.0 equiv), the 1H NMR signals corresponding to SbF6−⊂2 were observed to disappear, accompanied by the appearance of new host–guest peaks of SbF6−⊂1 and concomitant disappearance of the peaks for empty 1 . The addition of acid thus resulted in the selective disassembly of SbF6−⊂2 and release of its cargo SbF6−, which was then encapsulated by cage 1. Subsequent addition of the base DIPEA (9.0 equiv) generated new 1H NMR signals corresponding to empty 2. The transfer of SbF6− from host 2 to host 1 was thus achieved, mediated by acid and base.Based upon the observations above, we designed the system shown in Figure 2 to 1 thus took place over a time scale of minutes via the acid‐base accelerated process shown in Figure 6− delivery from 2 to 1 was slow due to kinetic trapping of the cargo within 2. After mixing SbF6−⊂2 and 1, only 30 % of the SbF6− transferred from 2 into 1 after 3 h, and 80 % of SbF6− was delivered after 45 h . Complete cargo delivery from 2 to 1 thus required the acid–base cycle shown in Figure The thermodynamically favored cargo transfer from 1 and 2 also occurred between 1,3‐dioxane⊂1 and SbF6−⊂2 . The SbF6− released from cage 2 following acidification displaced the more‐weakly bound 1,3‐dioxane guest from 1, forming the new complex SbF6−⊂1. Subsequent addition of DIPEA (10 equiv) brought about the reformation of 2, which took up the released dioxane from solution to generate 1,3‐dioxane⊂2. Thus, by using acid and base as chemical stimuli the cargo SbF6− was transferred from cage 2 to cage 1, and the cargo 1,3‐dioxane was correspondingly moved from the cavity of 1 to that of 2, with the whole process occurring on a time scale of minutes.The rapid exchange of cargoes between tetrahedra 2 Figure . During 1 had taken up SbF6− in this case after 81 h, with the other 18 % of 1 binding the original 1,3‐dioxane cargo .This result contrasted with the observation of a control experiment in which no acid–base cycle was carried out. Only 82 % of The strategy for improving the acid resistance of coordination cages developed herein may well allow other functional capsules to be constructed, in turn permitting more complex tasks to be carried out within systems of capsules.The authors declare no conflict of interest.As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re‐organized for online delivery, but are not copy‐edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.SupplementaryClick here for additional data file.


At present, the product of solar N2 fixation is either NH4+ or NO3−. Few reports described the simultaneous formation of ammonia (NH4+) and nitrate (NO3−) by a photocatalytic reaction and the related mechanism. In this work, we report a strategy to photocatalytically fix nitrogen through simultaneous reduction and oxidation to produce NH4+ and NO3− by W18O49 nanowires in pure water. The underlying mechanism of wavelength-dependent N2 fixation in the presence of surface defects is proposed, with an emphasis on oxygen vacancies that not only facilitate the activation and dissociation of N2 but also improve light absorption and the separation of the photoexcited carriers. Both NH4+ and NO3− can be produced in pure water under a simulated solar light and even till the wavelength reaching 730 nm. The maximum quantum efficiency reaches 9% at 365 nm. Theoretical calculation reveals that disproportionation reaction of the N2 molecule is more energetically favorable than either reduction or oxidation alone. It is worth noting that the molar fraction of NH4+ in the total product (NH4+ plus NO3−) shows an inverted volcano shape from 365 nm to 730 nm. The increased fraction of NO3− from 365 nm to around 427 nm results from the competition between the oxygen evolution reaction (OER) at W sites without oxygen vacancies and the N2 oxidation reaction (NOR) at oxygen vacancy sites, which is driven by the intrinsically delocalized photoexcited holes. From 427 nm to 730 nm, NOR is energetically restricted due to its higher equilibrium potential than that of OER, accompanied by the localized photoexcited holes on oxygen vacancies. Full disproportionation of N2 is achieved within a range of wavelength from ~427 nm to ~515 nm. This work presents a rational strategy to efficiently utilize the photoexcited carriers and optimize the photocatalyst for practical nitrogen fixation.Solar-driven N Therefore, the overall reaction is as follows:Either NHcatalyst , 14, in 2 can also be oxidized to NO3− over pothole-rich ultrathin WO3 nanosheets [3− and NH3 could be produced simultaneously, with N2 fixation proceeding through the following reactions:The voltage per electron is 1.13 V for the above reaction. Previous work has indicated that Nnosheets . It is r2 is removed from the reaction system, the maximization of NO3− will correspond to the consumption of all produced oxygen, which gives the overall reaction as follows:The voltage per electron is 1.57 V for Reaction , meaning2 fixation is the activation and dissociation of the extremely stable N≡N triple bond (bond strength of ~941 kJ mol−1) [2 fixation is to efficiently transfer the energetic photoexcited electrons to the rather inert N2 molecule [π∗-orbitals of the nitrogen molecule [2 molecule can be chemisorbed for facile electron access. Such sites serve as the effective bridge between the energetic photoelectrons and the nitrogen molecule [2 fixation efficiency. On the other hand, the appropriate anion vacancies in the bulk and on the surfaces of semiconductor photocatalysts can facilitate the separation and migration of the photogenerated electrons and holes [It is an established understanding that the rate-determining step for NJ mol−1) , 16, 17.molecule . The N≡Nmolecule , 18. Formolecule . Surfacemolecule  can effemolecule , 21. Divmolecule , 14, 18,molecule , 23, andmolecule –26, havend holes , which ind holes , 18. Thend holes –30, thus18O49 nanowires with distorted surface structures containing abundant surface oxygen vacancies were synthesized using a simple solvothermal method and are intended as a prototype for studying the wavelength-controlled N2 fixation in the presence of surface defects. The as-synthesized sample showed photocatalytic activity for N2 fixation to NH4+ and NO3− in pure water from ultraviolet up to near the end of visible light (730 nm) and exhibited high performance under simulated solar light (AM 1.5G) irradiation. The quantum efficiency (QE) reached about 9% at 365 nm through the simultaneous generation of both NH4+ and NO3−. Both experimental and theoretical results suggested that surface oxygen vacancies serve as catalytic sites and are essential for the high efficiency of N2 fixation. The oxidation of N2 was found to be retarded at either sufficiently short or sufficiently long wavelengths, and full disproportionation of N2 through Reaction  (PDF 05-0392) as previously reported [18O49 consists of ultrathin nanowires  pattern demonstrates that the diffraction rings belong to the  planes of the W18O49 structure  is presented in 4+ and NO3− within 12 h were about 22.8 μmol L−1 gcat−1 h−1 and 0.54 μmol L−1 gcat−1 h−1, respectively. W18O49 nanowires were also tested under irradiation of a 300 W xenon light (872 mW/cm2). The average NH3 production rate was about 65.2 μmol L−1 gcat−1 h−1, and the yield rate of NO3− was nearly 0.57 μmol L−1 gcat−1 h−1 for the as-synthesized W18O49 nanowires  increases at 300°C under a 300 W xenon lamp and 5 W of 370 nm LED illumination, respectively. The standard curves for quantifying ammonia and nitrate concentrations were calibrated using ion chromatography, which is a precise measurement for most anions and cations. The correlation coefficient values are 0.9993 and 0.9974 for ammonia and nitrate calibration curves  during 427~515 nm; the reason will be discussed herein below.In order to understand the wavelength-dependent catalytic process for No 730 nm . Althougvs. wavelength follows an inverted volcano shape in the range from 365 to 498 nm  can also be evaluated based on the amount of photofixation products under LED light illumination using the equations , 2 in tho 498 nm . In thise Figure . The abs Figures  and S8c. Figures  and S8a.y Figure .218O in normal distilled water was used as the reagent. After 5 h of xenon lamp irradiation, the 18O isotope was quantified by the denitrification method using Delta V-Precon  to be about 0.20% in NO3−. The measured peak position, peak area, and atomic percentage are shown in Figure 18O49 photocatalyst (0.05 g) and Ar gas bubble under 300 W xenon lamp irradiation at 25°C  with the as-synthesized W18O49 photocatalyst (0.05 g) and N2 gas bubble without irradiation at 25°C . In the full range of XPS spectra, peaks at binding energies corresponding to O and W elements are clearly observed, and no impurities other than carbon are observed in the spectra  were used to investigate the oxygen vacancies and N2 adsorption on the surface oxygen vacancies. In g = 2.003 caused by oxygen vacancies in the as-synthesized and annealed sample for 30 min [2 begins at 450 K and centers at 604.6 K, of which the positions suggest chemisorption of nitrogen on the surface. A first-order process was indicated with the N2 peak unchanged with coverage for adsorption at 545 K. N2 was the major desorption product, with a peak at 650 K on Ru/Al2O3 [2 desorbed. For the annealed sample, the N2 TCD signal of the annealed W18O49 dramatically decreases in comparison with that of the as-synthesized sample, suggesting that there was a significant drop in the population of surface oxygen vacancies after annealing. In combination with the EPR and TCD results, it can be concluded that the surface oxygen vacancies are reduced but still expected to exist inside the annealed sample.Electron paramagnetic resonance (EPR) spectroscopy and temperature-programmed desorption of Nr 30 min . Thus, tRu/Al2O3 –46. Sinc18O49 nanowires for 30 min were examined in the wavelength range of 330-500 nm with an excitation wavelength of 280 nm at room temperature  are consistent with pervious work [2 fixation process. We found that the N2 molecule cannot be chemically adsorbed on a perfect W18O49 surface  and the corresponding energy (ΔGPDS) is 1.71 eV. In NOR, N2 can be oxidized to produce two NO molecules  with an oxygen vacancy and the pristine W18O49 (001) are conceived from studies of OER on other metal oxides and depicted in Figures GPDS for both pathways, OER appears to be more feasible on a facet without an oxygen vacancy. The formation of H2O2 was also examined  shows a gradual decrease from 365 nm to 427 nm, followed by an increase from 427 nm to 730 nm. This trend can be rationalized as follows: in the short wavelength range, the energetically favorable OER predominates at the W sites without a nearby oxygen vacancy due to the intrinsic absorption of the catalyst and the delocalized nature of the photoexcited holes; in long wavelength ranges, NOR becomes more energetically challenging as compared with OER at oxygen vacancies according to the equilibrium potential for both reactions. The photogenerated carriers are most efficiently utilized in the wavelength range from ~427 nm to ~515 nm. This work presents a new insight into the role of oxygen vacancies in the wavelength-dependent photocatalytic nitrogen fixation and demonstrates the underlying mechanisms that could guide the design of future photocatalysts of higher efficiencies.In summary, we have developed oxygen vacancy-rich W


Vibrio sp. HC0601C5) with iron and various metal ions in + 3 oxidation state in an octahedral (Oh) environment. To survive in the iron-deficient environment of their host, pathogenic bacteria have devised various efficient iron acquisition strategies. One such strategy involves the production of low molecular weight peptides called siderophores, which have a strong affinity and specificity to chelate Fe3+ and can thus facilitate uptake of this metal in order to ensure iron requirements. The Fe uptake by amphibactin and the release of iron inside the cell have been studied. Comparison of the interaction of different transition metal ions (M3+) with amphibactin has been studied and it reveals that Co and Ga form stable complexes with this siderophore. The competition of Co and Ga with Fe impedes iron uptake by bacteria, thereby preventing infection.We have studied the diversity and specificity of interactions of amphibactin produced by Vibrio genus bacterium ( The Vibrio genus is curved-rod shaped gram-negative bacterium that is found in estuarine and marine environments worldwide. Several species of this genus can cause foodborne infection9. The seawater environments that are home to Vibrionaceae are slightly alkaline (pH 7.5–8.4), and the total concentration of soluble means Fe+++, FeOH++, Fe(OH)2+, Fe++, and FeOH+ in the absence of any chelating ligands is as low as 10–10 M, which is less than the amount required for bacterial growth (10−6–10−7 M)12. In biological systems, these Fe levels are further reduced (10−15–10−25 M) through sequestration by molecules such as transferrin and lactoferrin. For biological processes, Fe is required in a + 2 oxidation state. In aqueous-aerobic conditions and neutral pH, Fe is present mostly as insoluble Fe(III) hydroxide, which cannot be taken up by microorganisms14. In response to Fe scarcity and high biological demand, microorganisms have evolved strategies to acquire iron from the environment. In this regard, microorganisms secrete small-molecule peptides called siderophores, which chelate Fe3+, thereby ensuring their capacity to maintain biological processes18. Maintaining a dynamic equilibrium of Fe availability for the cell, i.e., Fe homeostasis is therefore critical for optimal cellular function, and indeed for life. Siderophores are metal-chelating agents with low molecular masses (200–2000 Da) produced by microorganisms and plants, especially under Fe-limiting conditions19. Several hundred siderophores, varying considerably in chemical composition, have been isolated and characterized. In this regard, they can be classified as hydroxycarboxylate-, catecholate-, or hydroxamate-type on the basis of the acidic moieties they hold in their metal-binding sites2.Metal ions are present in all microorganisms in many complexed forms, and they play key roles in numerous biological processes. Further studies of metal ion uptake by microorganisms are expected to shed more light on their life cycles and survival in different environmental conditions. The element Fe is essential for the growth of almost all microorganisms because it catalyzes several enzymatic processes, oxygen metabolism, electron transfer, and DNA and RNA syntheses, among others24. The formation of Fe3+–siderophore complexes is affected by pH because of competition between free protons and Fe3+ ions for the free siderophore ligands25. In nature, Fe3+ competes for the siderophore binding sites not only with free protons but also with other metal ions, such as divalent cations Cd2+, Cu2+, Ni2+, Pb2+ and Zn2+, trivalent cations Mn3+, Co3+ and Al3+, and actinides Th4+, U4+ and Pu4+27. Several studies have shown that siderophores influence the mobility of these metal ions in the environment28.The prime role of siderophores is to scavenge Fe. However, these small bioactive molecules also form complexes with other essential elements , thereby mobilizing them and making them available for microorganismsVibrio sp. HC0601C5  from the environment, transport it into the cell, and then release it for cellular functions. Here we studied how amphibactin binds to Fe3+ and other + 3 oxidation state metal ions and whether this siderophore has greater affinity to bind metals other than Fe3+. Computational quantum chemistry tools can provide insights into the energetic parameters of metal complexation with amphibactin, the metal specificity of amphibactin, the metal–amphibactin interaction, the redox reaction, and the release of the Fe–amphibactin complex. Here we have computed different parameters to understand the binding of different M3+ ions with amphibactin and tried to deduce from these calculated parameters why certain M3+ ions form stable complexes with amphibactin. Fe is essential for many metabolic processes in microorganisms and developing an effective strategy to limit access to this metal will be a good defense against bacterial infections39. Several strategies to inhibit bacterial infections have been reported, and the research community faces the major challenge of antibiotic resistance of drugs42. In this context, the relative stability, interaction energy and affinity of the chelator amphibactin with various transition metal ions in + 3 oxidation state, other than Fe, are studied in order to examine the potential of using amphibactin–metal ion interaction as a tool to develop new drugs for antibiotic resistance. In this regard, here we explored the antibacterial activity of vibrio genus bacterium (Vibrio sp. HC0601C5) based on the chelation of metal ions Co3+ and Ga3+ which have similar ionic radii as Fe3+ with amphibactin. We demonstrate that the bacterial Fe uptake transport system can be exploited to deliver antimicrobials based on Co3+ and Ga3+ to the intracellular space of target bacteria with high specificity. This approach impedes Fe uptake and therefore blocks cellular processes.In recent years, a novel family of cell-associated amphiphilic siderophores called amphibactin has been reported in marine gram-negative bacterium 3+ prefers a hexa-coordinate octahedral ligand coordination sphere. The amphibactin–Fe(III) is a high spin d5 complex. Amphibactin has three hydroxamate ends; three of these groups bind Fe3+ in an Oh geometry, forming a neutral 1:1 complex with a single unpaired electron centered on the Fe43. Figure Fe3+/Fe2+ and various transition metal ions in + 3 oxidation states by calculating and analyzing the parameters discussed below. The 1st row transition metals (Sc–Co), the Fe group  and Mo, all of these with a preference for + 3 oxidation states and octahedral (Oh) geometry, were examined.The geometric parameters of the optimized local minimum structures of amphibactin–metal ion complexes are given in Fig. 44. The energy of the HOMO (EHOMO), energy of the LUMO (ELUMO) and the HOMO–LUMO gap (ΔEH–L) are used to describe the global reactivity and kinetic stability of a system48. The higher the value of ΔEH–L, the lower the reactivity of a molecule and vice versa. To evaluate the chemical reactivity or kinetic stability, the ΔEH-L of all twelve amphibactin–transition metal ion complexes was calculated at B3LYP and M06/DEF2TZVP level (Table H-L was as follows: Ga3+ > Sc3+ > Cr3+ > Mn3+ > Co3+ > V3+ > Fe3+ > Ti3+ > Mo3+ > Ru3+ > Fe2+ > Os3+ (B3LYP/def2tzvp level). At higher level calculation (M06/def2tzvp level) the order of decreasing ΔEH-L gap was as follows: Ga3+ > Sc3+ > Cr3+ > Co3+ > Mn3+ > V3+ > Fe3+ > Mo3+ > Ti3+ > Ru3+ > Os3+ > Fe2+. The amphibactin–Ga3+ complex had the highest ΔEH–L, and hence was the most kinetically stable complex, the least stable being the amphibactin–Fe2+ and amphibactin–Os3+ complex from B3LYP/M06/def2tzvp calculations. Ionic radius of the metal ion is an important factor for amphibactin chelation with the metal ion. Here Sc3+ with high ΔEH–L gap, but with large ionic radius compared to Fe3+ ion results in reduced preference for complexation with amphibactin  value  in an Oh geometry. The high spin d2 V3+ also showed high ΔEH–L than Fe3+ due to high LFSE it had in an Oh environment. The Mn3+ shows a higher ΔEH–L gap, but the d4 high spin t2g3 eg1 Mn3+ ion was unstable and readily decomposes to Mn2+ and Mn4+ in aqueous condition49. The Co3+ had large ΔEH-L gap value as it forms stable Oh complex with amphibactin. The optimized structure of the amphibactin–Mo complex was broken with the loss of metal–ligand six-coordinate Oh geometry. The results from Table 3+, amphibactin–Fe3+/Ga3+/Co3+/Cr3+/Mn3+ complexes were the most kinetically stable or were less reactive than other complexes.The ground state reactivity was analyzed for amphibactin–transition metal ion complexes from the frontier molecular orbitals (FMOs): HOMO  and LUMO el Table . The ord54. According to the Hard and Soft Acid and Bases (HSAB) principle, a hard acid prefers a hard base and a soft acid prefers a soft base. Here, free Fe3+ has an ionic radius of 67 pm and acts as a “hard” acid, preferring “hard” oxygen ligands such as phenolate (from Tyr) and carboxylate (from Asp or Glu). Free Fe2+ has an ionic radius of 83 pm and is borderline between a “hard” and “soft” acid, favoring coordination of nitrogen atoms (from His or pyrrole) and sulfur ligands (from Cys or Met) over oxygen ligands55. Since the parameter η indicates a preference of a hard/soft acid for a hard/soft base, for our purposes it provides a quantitative value of the preference of the chelator amphibactin for distinct metal ions.Chemical hardness (η), first put forward by Pearson, is a measure of the resistance of a chemical species to change its electronic configuration3+ with large ionic radius  between amphibactin and the different transition metal ions were calculated using the following equationEion–amphibactin is the energy of the ion–amphibactin complex, Eamphibactin is the energy of the isolated amphibactin, and Eion is the energy of the isolated metal ion. The larger the negative interaction energy, the stronger the intermolecular interaction between amphibactin and the transition metal ion. The Eint with ZPE and BSSE correction for all the amphibactin–metal complexes are reported in Table 3+ ions (~ 64 pm). The Fe3+, Co3+, Ga3+, and Cr3+ have similar ionic radii around (62–64 pm) and the ionic radii of Mn3+ and V3+ were next closer to Fe3+. Among these six metal ions the order of Eint was Co3+ > Fe3+ ~ Mn3+ > Ga3+ > Cr3+ > V3+.The amphibactin–Fe3+/Co3+/Ga3+/Mn3+ complexes showed large negative Eint values, with Co3+ having maximum interaction energy  preferred a tetragonal coordination compared to Oh due to Jahn–Teller effect  showed lower Eint values and larger ionic radii.Interaction energies  are derived by subtracting the complexation energies  from the interaction energy value . The Erelax values for the amphibactin–metal complexes are given in Table h geometry) from the preferred conformation of amphibactinRelaxation or deformation energies . The ionic radii of Mn3+ and V3+ were next closer to Fe3+. The order of relaxation energy (δ) is Co3+ > Mn3+ > Cr3+ > V3+  > Fe3+ > Ga3+ at M06/def2tzvp level. The metal ions Ru3+, Os3+, Sc3+, except  had low values of Erelax. The inducing effects of the ions on the conformation of amphibactin also depended on the strength of the amphibactin–metal ion interactions. This observation may explain why Cr3+, Mn3+ and V3+ showed slightly higher. The high spin d4 Mn3+ (~ 66–67 pm) with a stable tetragonal geometry compared to Oh due to Jahn–Teller effect causes two of the bond move apart and other four Mn-ligand bonds to come closer , the tetrahedral geometry is preferred compared to Oh. For a metal ion to induce an Oh geometry causes more Erelax and hence this may be the reason for higher Erelax value for Cr3+ than Ga3+. The high spin d2 V3+ also has higher preference for Oh geometry than Ga3+ and therefore a higher Erelax value. Therefore from above the discussion, Co3+ metal ion had the largest Erelax values, thereby making it the most stable Oh complexes, Fe2+ being the least stable with lowest Erelax. The Erelax values decreased with the increase in the atomic radii of the ions upon complexation with amphibactin. The Mo3+ does not retain an Oh geometry after optimization (one of the bonds is broken) and the high δ value accounts for that broken bond.The large the value of er Table . This moEel is the electronic energy obtained from the SCF (Self Consistent Field) computation and Evib include the Zero point energy and temperature corrections from 0 to 298 K obtained by the thermo-chemical analysis of vibrational frequencies61. MIA is considered as the negative of the enthalpy for the dissociation of the amphibactin–metal complex to free amphibactin and metal ion. The higher the MIA value, the greater the affinity of the metal ion for amphibactin. MIA values of the amphibactin–metal complexes showed a similar trend to the Eint values  metal ions with almost same ionic radii, the order of MIA are: Co3+ > Fe3+ ~ Mn3+ > Ga3+ > Cr3+ > V3+. The Mn3+ with its d4 high spin tetragonal structure promotes better metal–ligand interaction and hence the large MIA value. The decreased metal–ligand interaction in case of Cr3+ and V3+ results in low MIA. The higher values for MIA for Ru3+ and Os3+ may be due to high (LFSE) expected in these complexes due to more interaction between the ligand and diffuse valence metal orbitals. These distorted Oh structures were less stable which is evident from their relaxation energies  is one of the methods to study the stability of metal–ligand interactions and was calculated as,entclass1pt{minimaentclass1pt{minimaes Table . Out of h toward the trigonal prism with smaller α. As shown in Table 3+, Ga3+, Mn3+, Cr3+ and Co3+ were close to 90°, as required for an Oh coordination sphere, thus making these metal ions more stable than others with a smaller bite angle. The decreasing order of α: Co3+ > Mn3+ > Ga3+ ~ Cr3+ > Fe3+. The bite angles for remaining metal ions were farther away from 90°, thus indicating a more deviation from Oh geometry. If ligands were large; so as to avoid ligand-ligand repulsion, for metal ions  with zero LFSE , the tetrahedral geometry was preferred over Oh. These metal ions have showed deviation from Oh geometry  of the chelate ring and is sensitive to the metal–ligand distance. The bite angle α is defined as the L–M–L angle Fig. . The lonry Table . The Co33+ and Co3+ as the metal ions with the largest ∆G/∆H values, thereby allowing them to form strong complexes with amphibactin. In contrast, Fe2+ was the least stable metal ion, as reflected by the lowest ∆G/∆H values. The ∆G/∆H values depended on the value of ∆S. Large negative ∆S values were found for Ga3+, Co3+, Fe3+, Mn3+, Os3+ and Ru3+. We calculated the individual contributions to total ∆S. The ∆Strans and ∆Srot became more negative as the size of the complex grew and is purely size-dependent. This explains the reason for large negative ∆Strans values for Os3+ and Ru3+ complexes because as we go down the periodic table the size increases due to more diffuse orbitals. The ∆Srot depends on the symmetry and geometry of the complex formed. If the resulting complex has highly symmetric, like Oh geometry the ∆Srot will be more negative. From Table 3+, Fe3+, Ga3+, Cr3+ and Mn3+ had larger negative ∆Srot values implying that the complexes formed by these metal ions have more symmetric Oh geometry and contributes to its stability. Also the bite angles calculated for above mentioned metal ions were closer to Oh geometry. The ∆Svib depended on the strength of the interaction between the metal ion and amphibactin. As the complex became stronger, the vibrations became stiffer, and the ∆Svib became more negative. In case of Ga3+, Co3+, Fe3+, Cr3+, Mn3+, the ∆Svib values were high, indicating strong amphibactin–metal interactions in these complexes. The ions Cr3+, Sc3+, Ti3+, Os3+ and Ru3+ had high ∆Svib but with low ∆G values. The high ∆Svib value for Cr3+ may be due to the high LFSE value exhibited by Cr3+ in Oh coordination, but the weak metal–ligand interaction results in low ∆G value. In the case of Sc3+ and Ti3+ as well, the high LFSE in Oh environment contribute to high ∆Svib values. The higher penetration effect in Os3+ and Ru3+ assist in better metal–ligand interaction and hence higher ∆Svib values for these ions. The Mn3+ also formed a stable complex with amphibactin. However, Mn3+ complexes are generally unstable in aqueous neutral and acidic pH environments and they decompose in water to produce Mn2+ and Mn4+58. Also Mn3+ prefers a tetragonal geometry in d4 state62. In tetragonal geometry either two ligands move apart or come closer to the central metal ion to reduce the degeneracy. In amphibactin–Mn(III) complex two of the bond distances showed considerable difference compared to other four Mn–ligand bonds  of the transition metal ions complexed with amphibactin are reported in Table ds Table . The the3+ to Fe2+ is an important step in the Fe uptake process. A greater understanding of this step may contribute to the development of molecules that inhibit Fe uptake. All the following calculations were carried out at B3LYP/6-31g/LANL2DZ level in gaseous and aqueous condition (dielectric constant ε = 78.4) in G09 CPCM model.A powerful strategy to fight microbial infections is to prevent pathogens from acquiring Fe. The reduction of Fe2+ for metabolic processes in the following two ways63.The molecular weights of the ferric–siderophore complexes exceeded the cut off for porins and therefore require specific outer membrane receptors for their uptake into the cell through the periplasmic space. Once siderophores enter the cytoplasm, the Fe from the ferric-siderophore complex can be released as Fe2+ in to the cell cytoplasm  to amphibactin–Fe(II) complex with zero point correction in aqueous solvent 3+ to amphibactin–Fe2+. This was compared with standard hydrogen electrode (SHE) using Eqs.  are proteins that are localized and imbedded in the plasma membrane of the Gram-negative bacterium are responsible for the pH dependent binding and release of the substrate and for other reactions like reduction65. Many vibrio species use NADH with ferric reductase enzyme72. Inside the cell, NADH acts as a potential electron donor for the enzyme. Therefore we can couple the reduction reaction of amphibactin–Fe3+ to amphibactin–Fe2+ with NADH oxidation reaction. The overall redox reaction is the sum of the two half-cell reactions or couples: (a) reduction of amphibactin–Fe3+ to amphibactin–Fe2+ and (b) oxidation of NADH → NAD− + H+. We calculated the above mentioned two half-cell reactions. hcell at pH = 7 was calculated from the Nernest equations  by NADH was the same 0.12 V  to amphibactin–Fe(II) at pH = 0, E0 = 0.44 and at pH = 7, Eh = 0.02588 respectively are different and Eh < E0  to amphibactin–Fe(II) has a free energy value of 110 kcal/mol. Therefore it might not be feasible to couple with NADH reduction but it would be favourable  to couple with an easy-to-reduce and less energetic molecule FADH2. With FADH2 (free) as reducing agent, the Ecell = 0.22 V (Eq. 2 (bound) Ecell = 0.41 V (Eq. H = 7 indicating the reduction of amphibactin–Fe(III) to amphibactin–Fe(II) is spontaneous and favoured.The reduction of amphibactin–Fe(III) to amphibactin–Fe(II) complex, followed by protonation and hydrolysis to release Fesee Fig. . The fir The Eq.  (Suppleming Eqs.  and S3)2+ in to  see Eq. . A negatquations –S10. Thet pH = 7 . The E°c2 V Eqs.  and S16. E0 Eqs.  and S10.32 V Eq.  indicatiial Eqs. –23. The /mol Eq.  is sligh/mol Eq.  at pH = 22 V Eq.  and FADH41 V Eq.  at a pH 2+ complex by three hydrogen atoms in aqueous medium was calculated using Scheme 2+ complex with three hydrogen atoms added to the (N–O)hydroxamate group coordinated Fe2+ metal ion in aqueous medium.Further protonation of the reduced amphibactin–Fe3+ followed by reduction reaction. The free energy change for the protonation reaction of amphibactin–Fe3+ with three hydrogen atoms attached to the (N–O) hydroxamate group in aqueous medium was calculated using Scheme The protonation of amphibactin–FeH = 7, the ∆G for Schemes At physiological pEH–L, chemical hardness (η), Eint and relaxation energy were calculated for amphibactin–Fe3+, amphibactin–Fe2+, 3H protonated amphibactin–Fe2+ and 6H protonated amphibactin–Fe2+ respectively 75. The energy for protonation of O of CO 7.44 kcal/mol higher than protonation of O of NO of hydroxamate group implying NO protonation was more preferred compared to CO protonation. Here a proton (H+) was attached to one of the O of CO of hydroxamate group of the three hydrogen protonated at three O atoms of NO of hydroxamate group amphibactin–Fe(II)–3H complex to get amphibactin–Fe(II)–4H complex. Computationally from G09 the pKa for hydroxamate CO calculated from the Eq.  or sulphur . Therefore, the reduction of amphibactin–Fe3+ (1) to amphibactin–Fe2+ (2) drastically lower the affinity of the siderophore for the Fe2+ ion. The Eint also decreases down Table 4. This implies that Fe3+ (1) reduction to Fe2+ (2) followed by subsequent protonation (3 and 4) reduce the affinity of siderophore for Fe2+ ion, thereby releasing the Fe into the cell. The Fe-free siderophore is usually degraded or recycled by excretion through an efflux pump system (like H+/Na+ driven pump). Further hydrolysis of amphibactin–Fe2+–3H is a spontaneous process with a ΔG = − 517.16 kcal/mol.The Δly Table . The pro the Eq.  was aroupH 7.5–8.75. The epH 7.5–8.75. The e2+(Fe(H2O)62+) was stable, with a ΔEH–L value of 5.77 eV, and can therefore be further used for metabolic processes inside the cell.The resulting aqua complex of Fe3+ complexes gained special attention for the treatment of infections associated with bacterial biofilms26. Ga3+ readily forms poly-hydroxo complexes in aqueous physiological conditions. Many chelated complexes of Ga3+ show antibacterial activity against Pseudomona aeruginosa and are stable in physiological conditions83. In addition to complexation, co-administration of Ga3+ salts with known antimicrobial agents, such as a combination of antimicrobial and non-anti-microbial agents, has been described to enhance antimicrobial potency85. A very small number of Co3+ complexes have biochemical roles. The Co3+ ion as such is unstable in water but can be stabilized against reduction to Co2+ by coordination to ligands or chelators. To date, only the N, O donor ligand type has been found to stabilize the Co3+ ion in aqueous conditions. The Co3+complexes derived from this ligand donor set have proved to be surprisingly efficient antibacterial or antiviral agents. Some of the most promising classes of Co3+ complexes containing N, O donor ligands, like Schiff base [Co(NH3)6]Cl3, are antibacterial and thermally and kinetically stable in aqueous solution, in addition to being easily synthesized88. The amphibactin is produced by bacteria to specifically chelate Fe3+ for biological process and hence the size of metal ion is an important factor. Our earlier analysis on the Eint, MIA, chemical hardness, ΔEH–L, and thermodynamic parameters /Co(III) complex is kinetically inert for further replacement reaction and the bacterial cell wall will allow its passage as the size is similar to Fe3+ ion. Since Fe is essential for the metabolic activities of bacteria and hence for their survival, the better complexation of amphibactin with Ga3+ and Co3+ than Fe3+  will lead to competition for Fe acquisition by bacteria. So instead of Fe; Ga and Co form stable complexes with amphibactin, thereby impairing bacterial metabolic activities and causing cellular toxicity, since the entered Co3+ and Ga3+ cannot partake in the oxidation–reduction processes inside the cell. The free energy changes for the following reactions were studiedAn alternative approach to block Fe uptake to limit pathogen growth is to use the bacteria’s Fe uptake systems against them in a “Trojan-horse” strategy. Various Gas Tables  and 2 fo3+ and amphibactin–Ga3+ complexes were thermodynamically feasible. The Co3+ was inert in aqueous condition but the replacement of monodentate ligand by multidentate was very favourable thermodynamically due to chelation effect. Entropy was largely responsible for the greater free energy change observed for chelates, compared to complexes of unidentate ligands with the same metal ion. The Co-hexamine was kinetically inert (high ΔEH–L = 6.625) in aqueous solution as it was a low spin d6 Oh complex with high LFSE. Instead of the Co-hexamine we can use [Co(CO3)3]3− complex (ΔEH–L = 5.14) as it is kinetically less stable or more labile making the forward replacement reaction kinetically feasible. The ∆G + ZPE = − 117.21 kcal/mol for Eq. (89.The ∆G with ZPE correction for Eqs. 3+ from the Co(NH3)6 complex and Ga3+ from the Ga(H2O)6 complex readily binds to amphibactin, forming thermodynamically stable amphibactin–Co and amphibactin–Ga complexes, which inhibit Fe uptake by the bacteria. Also, the different parameters calculated , metal ion affinity (MIA), relaxation energy (δ) and thermodynamic parameters  calculated indicate that out of the different metal ions studied  were high spin and remaining were low spin complexes. The input structure of amphibactin is made maintaining the (DDLL) configuration at asymmetric carbon centres as given in Fig. int), metal ion affinity (MIA), and relaxation energies were further calculated using appropriate equations. The Eint, MIA, relaxation energies were ZPE corrected. The Eint was calculated after correcting the basis set super-position error (BSSE) by the counterpoise procedure (CP) of Boys and Bernardi100. Geometry optimization was done, followed by vibrational frequency analysis of amphibactin–Fe2+ and amphibactin–Fe3+ at 298 K and 1 atm., in aqueous medium (dielectric ε = 78.4) using the polarized continuum (overlapping spheres) model (CPCM), where a calculation was performed in the presence of a solvent by placing the solute in a cavity within the solvent reaction field102.Density functional theory (DFT) calculations using the GAUSSIAN 09 suite of programs were carried out for all the amphibactin–metal complexesSupplementary Information.


The recent progress provides answers to long-held questions, identifies intriguing new behaviours, and opens up fresh questions for the field of transcription.Prokaryotic transcription is one of the most studied biological systems, with relevance to many fields including the development and use of antibiotics, the construction of synthetic gene networks, and the development of many cutting-edge methodologies. Here, we discuss recent structural, biochemical, and single-molecule biophysical studies targeting the mechanisms of transcription initiation in bacteria, including the formation of the open complex, the reaction of initial transcription, and the promoter escape step that leads to elongation. We specifically focus on the mechanisms employed by the RNA polymerase holoenzyme with the housekeeping sigma factor σ  Transcription is a fundamental process in all living organisms and serves as the first step in the flow of information from genes to functional molecules such as proteins or RNAs. Transcription in all organisms is highly regulated to ensure the right genes are expressed at the right places and in the amounts required for proper functioning of the cell 70 (so named due to its molecular weight of 70 KDa) in E.coli and the σA in T. thermophilus. In the early 1980s, Losick and coworkers discovered that most bacteria contain multiple proteins having high sequence homology to σ factors, and these different types of protein cofactors may associate with the RNA polymerase and result in switching between sets of promoters thus altering the global transcriptional landscape of the cell 70/σA dependent transcription initiation regulation and mechanism arising from biochemical, structural and single molecule studies.The protein machine at the heart of transcription is the RNA polymerase (RNAP), which can function alone or with other co-factors to copy information encoded in DNA to synthesise a RNA molecule. Despite the fact that the RNAP can, in principle, perform transcription from any DNA sequence, transcription was shown to initiate from specific DNA sequence elements called promoters inside the bacterial cell RNAP is conserved among all organisms. The bacterial, archaeal and eukaryotic RNAP are all members of a conserved protein family, named the “multi-subunit RNAP family” T.Aquaticus was solved in the late 1990s, followed by the structure of the RNAP core enzyme from E.coli2+ at its base. The β’ subunit makes up one pincer, termed the “clamp,” and part of the base of the active-centre cleft. The β subunit makes up the other pincer and the other part of the base of the active-centre cleft. In addition to the active-centre cleft, the RNA polymerase structure has two more channels: the secondary channel , and the RNA exit channel (which can accommodate a growing nascent RNA chain).The first structure of a complete multi-subunit RNAP core enzyme from E.coli promoters requires RNAP association with σ factor; however, free σ70 does not bind DNA 70 using crosslinking and FRET-based methods showed that free σ70exists in a compact conformation and upon association with core RNA polymerase, σ70 undergoes a large conformational change that unmask regions in the protein that could bind DNA 70 family of proteins came from X-ray crystallography studies of different domains of σ70 (from E.coli) and σA (from T. thermophilus) 70 and the RNAP core outlined the organisation of σ70 with respect to the core enzyme 70, their interactions with the core enzyme, and their organisation in the holoenzyme 70 contains five conserved regions: σR1.1, σR2, σR3, σR3.2 , and σR4. The σR2, σR3 and σR4 are structured, modular domains linked by flexible linker elements, while σR1.1 and σR3.2 are unstructured negatively charged domains Transcription initiation from The specific DNA sequences from which the bacterial RNAP holoenzyme initiates transcription are called promoters 70-dependent transcription initiation, two main consensus promoter sequences have been identified: the − 35 hexamer (5’-TTGACA-3′) and the − 10 hexamer (5′-TATAAT-3′), where numbers represent position upstream of the transcription start site (denoted as + 1) For σ70, resulting in increased open complex lifetimes In addition to these elements, it has been shown that DNA upstream of the − 35 hexamer  could play an important role in establishing contact with the αCTD of the core RNAP and may have significant effect on rates of open complex formation and transcription initiation o) has been extensively studied using crosslinking, systematic FRET, crystallography and cryo-EM. The studies show that in the open complex, the negatively charged domain σR1.1 is displaced from the RNAP active site, which then accommodates single strands of DNA in the active site cleft RM) may interact with adjacent DNA-bound transcription factors (such as the phage λ cI repressor). The σR2.3 interacts with the − 10 region of the promoter, where it makes specific contacts with bases at − 11 and − 7 by flipping them into proteins pockets in σ70, while it interacts non-specifically with other bases along DNA. The σR1.2 element contacts a “discriminator” element in the non-template strand of the promoter just downstream of the − 10 element . Although the number of conformations identified and the kinetics of the individual steps at different promoters may vary, an overall picture has emerged which identifies three important steps: the initial binding of RNAP holoenzyme to promoter DNA resulting in formation of a heparin-sensitive early intermediate I1 where the promoter DNA is in double-stranded form (heparin is a poly anion commonly used in transcription initiation studies as a competitor of promoter DNA), a slow isomerisation of I1 to a heparin-resistant intermediate I2 with a melted open DNA bubble (− 11 to + 2), followed by transformation of the initial unstable open bubble intermediate I2 to the final stable open complex (RPo)  A [31], [ex (RPo) .Fig. 2A 1 > I2 isomerisation step is only weakly dependent on salt concentration; it has thus been proposed that opening of the DNA bubble is not purely driven by the thermal dynamics of the dsDNA, but RNAP must play an active role in this step The slow rate-limiting I2) to stable open complex (RPo), however, vary greatly with urea and salt concentrations. It has been proposed that this may indicate large scale conformational changes in the RNAP involving folding of β’ jaw and other downstream mobile elements (DME) on the downstream promoter DNA duplex, as well as motions of the RNAP clamp that trigger closure of the active center cleft leading to formation of final RNAP-promoter open complex The final conversion of late intermediate  demonstrate that the polymerase accommodates single strands of DNA in the active center cleft. Access of double-stranded DNA to the active-centre cleft of RNA polymerase is restricted due to the narrow width of the cleft (< 20 Å) and the interactions of σR2 in and above the active centre cleft , which proposes that the RNAP active-centre cleft opens via a swinging motion of the β’ clamp, allowing double-stranded DNA to enter , which proposes that the melting propagates outside the active centre cleft, and that single-strands of unwound DNA enter the active centre cleft without any obligatory clamp opening , RNAP synthesises short RNA fragments, but instead of escaping from the promoter, RNAP releases short RNAs, reverts back to RPo has raised the possibility that for some promoters (e.g. rrnBP1), there may be scrunching in absence of nucleotides in the RPo leading to unusual transcription start sites. The crosslinking work also proposed that scrunching in RPo prepares the complex for efficient promoter escape and is a major determinant for ensuring high transcription turnovers at these promoters itc (one with a 5-mer RNA) shared different fates, with the non-template strand bulging out into the solvent, while the scrunched template strand remained within the polymerase creating stress on interactions with the β’ clamp and σR3.2 More recent studies using crosslinking approaches within RPThe σR3.2 finger was identified early on as an RNAP determinant of abortive initiation. This segment lies along the linker connecting σR3 and σR4, and passes through to the active centre cleft making contacts with template DNA lac promoter (−1G+1) resulted in greatly reduced pausing during initial transcription −10Y−1G+1) −10 element at the upstream end of the transcription bubble in the elongation pause is being substituted by the σR3.2 finger in the initiation pause. The observation of sequence dependence in the initiation pause is also in good agreement with previous studies which reported that promoters with certain sequence elements in the initial transcribing sequence tend to produce more abortive transcripts. A similar study using single-molecule assays of run-off transcript production on a similar lac promoter fragment also reported observation of long duration pausing during initial transcription ITC5. The next incoming nucleotide can then come in and bind at the i + 1 site resulting in its rapid incorporation to form a pre-translocated RPITC6. The σ3.2-template strand contacts limits scrunching upto 4 nt and 5′ end of the 6-nt RNA clashes with σ3.2, preventing translocation from the pre- to post-translocated state. At this point the complex enters an off-pathway paused state  and result in escape of RNAP from the promoter and entry into transcription elongation. It has been observed that there is a negative correlation between the strength of the promoter and the efficiency of the promoter escape, with stronger promoters generally resulting in relatively higher yields of abortive products and lower promoter escape efficiency 70 from RNAP.The structures of initial transcribing complexes reveal that the RNA transcript would emerge out of the RNA-exit channel of RNAP when it is longer than 15 nt. This corresponds to an RNA length that should result in repositioning of the σR3-σR4 linker element and of σR4 from their respective positions in RNAP, leading to proposals that, once the RNA reaches a sufficiently long length, it displaces the σR3-σR4 linker and σR4, facilitating promoter escape and dissociation of σThe ITS could affect promoter escape via the strength of the transcribed DNA/DNA hybrid and the strength of the resulting RNA/DNA hybrid; both factors play a role in determining open complex stability, and may also affect promoter escape efficiency. A more recent study used parallel Next Generation Sequence (NGS) approach to study the escape kinetics at a large set of ITS variants for four different promoter sequences 70 subunit following promoter escape; however, FRET-based studies on early elongation complexes found that σ70 could be highly retained in the elongating polymerase 70 retention in elongation complexes, and estimated the half-life of σ70 retention to be ∼ 50s 70 in elongating complexes may recognise some − 10 or − 35-like DNA sequence element in the transcribing gene, resulting in σ70-dependent pausing for the elongating polymerase Early studies proposed that the RNAP obligatorily lost the σ


Sequential in situ reactions take place between the β‐Zn4Sb3 additive and SnTe matrix, and an interesting “core–shell” microstructure (Sb@ZnTe) is obtained; the composition of SnTe matrix is also tuned and thus Sn vacancies are compensated effectively. Benefitting from the synergistic effect of the in situ reactions, an ultralow κlat ≈0.48 W m−1 K−1 at 873 K is obtained and the carrier concentrations and electrical properties are also improved successfully. Finally, a maximum ZT ≈1.32, which increases by ≈220% over the pristine SnTe, is achieved in the SnTe‐1.5% β‐Zn4Sb3 sample at 873 K. This work provides a new strategy to regulate the TE performance of SnTe and also offers a new insight to other related thermoelectric materials.Lead‐free chalcogenide SnTe has been demonstrated to be an efficient medium temperature thermoelectric (TE) material. However, high intrinsic Sn vacancies as well as high thermal conductivity devalue its performance. Here, β‐Zn 4Sb3 additive and SnTe matrix, and the resultant interesting “core–shell” structure is obtained in this work. The composition, microstructure, and transport properties of SnTe thermoelectric materials are synergistically tuned, so an ultralow lattice thermal conductivity (≈0.48 Wm−1 K−1 at 873 K) and relatively high ZT (≈1.32 at 873 K) are achieved, which present an effective method to enhance the thermoelectric performance of SnTe, and are also of referential values for other thermoelectric materials.In situ chemical reactions occur between the β‐Zn Our previous work demonstrated that it could remarkably reduce the phonon thermal conductivity and enhance the thermoelectric performance of p‐type 2Te3‐based materials by decomposing into Zn and ZnSb nanoinclusions.4Sb3 was incorporated into the matrix of SnTe to improve its thermoelectric performance. Very unexpectedly and interestingly, a special “core–shell” structure with Sb core and ZnTe shell (Sb@ZnTe) has been obtained. Benefitting from the in situ reaction and the associated “core–shell” microstructure, an ultralow κlat ≈ 0.48 W m−1 K−1 has been achieved while a relatively high power factor has also been maintained and thus a high thermoelectric performance with ZT of ≈1.32 has been obtained at 873 K for the SnTe‐1.5% β‐Zn4Sb3 sample. Notably, single doping and co‐doping with Zn and Sb have also been studied for comparison, and the results illustrated that only the β‐Zn4Sb3 containing samples show special “core–shell” microstructures and achieved higher TE performance. This work presents an effective method to enhance the TE performance of SnTe, which also offers a new insight to other related thermoelectric materials.β‐Zn22.1Figurex at% β‐Zn4Sb3  samples. The main peaks in all patterns can be well indexed to the cubic SnTe structure (PDF# 46‐1210). Besides that, blende ZnTe phase (PDF#03‐065‐0385) also shows up when the content of β‐Zn4Sb3 is higher than 1 at%. No peak of β‐Zn4Sb3 can be found in the XRD patterns, indicating that all the β‐Zn4Sb3 nanopowders have been decomposed during the process of spark plasma sintering (SPS) as consistent with the reported work,4Sb3 powder mixture before SPS, the first endothermic peak around ≈680 K corresponds to the decomposition temperature of β‐Zn4Sb3, and the second wide exothermic peak around 770 K indicates that another reaction was happened between the decomposition products and the SnTe matrix at elevated temperature, which should be ascribed to the formation of ZnTe phase, as depicted by the following equationFrom this reaction, the decomposition products are Zn and ZnSb, but why is there small amount of ZnTe phase but not ZnSb phase appear in the above XRD patterns? The differential thermal analysis (DTA) result in Figure 4Sb3 accompanies with the appearance of ZnTe and Sb phase once the temperature is over 723 K, which is in good agreement with the DTA results. It should be noted here that the sample with high content of 10% β‐Zn4Sb3 is chosen so that the reaction products can be well distinguished in the high temperature in situ XRD patterns, considering no peak of Sb is observed in the SPS samples , as listed in Table S1 in the Supporting Information, further confirms that the reaction is favorable in thermodynamics.2+ in ZnSb nanoparticles (NP) gradually combines with Te2− in SnTe matrix and results in the formation of the Sb@ZnTe core–shell structures, which is significantly conducive to the TE performance of SnTe and will be detailed below.2.2Figurex% β‐Zn4Sb3 samples, respectively. It can be seen that the pristine SnTe matrix demonstrates typical polycrystalline morphology  was employed to characterize the core–shell microstructure and the results are shown in 2.3Figurex at% β‐Zn4Sb3  samples. We can see that the resistivities (ρ) increase with increasing β‐Zn4Sb3 content, which can be illustrated by the carrier concentration reduction as listed in TablenH) of the pristine SnTe is ≈1.36 × 1020 cm−3 and gradually decreases to ≈7.4 × 1019 cm−3 for the sample with 2% β‐Zn4Sb3, which should be ascribed to the substitution Zn for Sn and the resultant Sn self‐compensation effect by the in situ reaction mentioned above.S, as shown in Figure 4Sb3 content in low temperature range, and then increases significantly with the content of β‐Zn4Sb3 when the temperature is over 600 K. This anomalous phenomenon should be attributed to the decrease of Sn vacancies caused by Zn alloying and Sn self‐compensation, which is consistent with the previous reported work.4Sb3 and the matrix, the Fermi level rises and gradually shifts away from the heavy valence band , only left the light‐hole band contributes to the Seebeck coefficient and thus results in a lower Seebeck value at low temperature range.x at% β‐Zn4Sb3 samples  shown in Figure x value. The κtot is essentially a combination of two parts: the electronic contribution (κel) and the lattice contribution (κlat).el = LσT, where L is the Lorenz number, σ is the electrical conductivity, and T is the absolute temperature.el can be found in Figure S4 in the Supporting Information. The κlat is then calculated by subtracting κel from κtot, and the results are shown in Figure lat decreases with the content of β‐Zn4Sb3 and the minimum κlat is only about 0.48 Wm−1 K−1 at 873 K for the SnTe‐2 at% β‐Zn4Sb3 sample, which is close to the amorphous limit.The total thermal conductivity (κs with respect to the phonon frequency (ω) has been calculated and presented in Figurelat.lat. In addition, the κlat was also calculated according to the well‐known Callaway model (refer to the Supporting Information) with consideration of all these hierarchical factors (U+EP+GB+PD+NP) in the SnTe‐β‐Zn4Sb3 sample as a reference to SnTe matrix  samples were effectively enhanced  and Sb powders (99.99 wt%) were weighed in the stoichiometric molar ratio, and sealed in an evacuated quartz tube, then melted at 1023 K for 24 h and quenched in cool water.−3 Pa) at 1123 K for 10 h, soaked for 12 h, and quenched to room temperature. Then the as‐melt ingots were crushed and ball milled into fine powders. After that, different content of β‐Zn4Sb3 powders were added to the SnTe powders  the powders were further mixed by ball milling at 250 rpm for 1 h. Finally, the powder mixtures were sintered and densified by SPS at 773 K for 10 min under a pressure of 60 MPa in a vacuum atmosphere.First, the SnTe was synthesized by melting the stoichiometric elemental mixture  in sealed quartz tubes , and the mixture powders were sealed in quartz tubes and sintered with the same methods mentioned above. The relative density of all the obtained samples was above 95%.For comparison, the corresponding content of Zn‐doped, Sb‐doped, and Zn/Sb co‐doped SnTe samples were also synthesized. High purity Zn shot and Sb powder were weighed in the stoichiometric molar ratio  were simultaneously obtained by using a Namicro‐III thermoelectric measurement system. The measurement uncertainties typically are 5% for the Seebeck coefficient and 3% for the electrical resistivity. The Hall coefficient (RH) was measured by the van der Pauw method with a HMS‐5500 Hall measurement system. Carrier density (nH) and mobility (μH) were calculated according to the relationship nH = 1/(e RH) and μH = σ RH, where σ is the electrical conductivity obtained from the Namicro‐III system. The thermal conductivity was calculated via κ = D Cp ρ, where the thermal diffusivity coefficient (D) was measured with a NETZSCH LFA‐427 laser thermal conductivity instrument and the heat capacity (Cp) was determined by the empirical formula Cp (kB per atom) = (3.07 + 0.00047 (T‐300)),The phase characterization was analyzed by powder X‐ray diffraction patterns . Field‐emission scanning electron microscope (NanoSEM 450), HRTEM, and energy‐dispersive X‐ray spectroscopy (EDS) observation of the selected specimens was performed with a JEOL JEM‐2100 transmission electron microscope. The DTA measurements were analyzed by using an STA449F3 (NETZSCH) equipment. The Seebeck coefficient, The authors declare no conflict of interest.Supporting InformationClick here for additional data file.