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It is shown that the chiral ligand glutathione can induce active surface growth in the deposition of Au on Au nanoplates, forming nano‐badges with complex surface patterns. The special feature of the growth mode is that the growth materials are diverted to a few active sites, causing deep valleys and high standing walls. The circular dichroism signal depends on the tilting degree of the walls, which likely arises from the different packing of the chiral ligands on the two pro‐chiral slopes. As a characteristic sign of the Active Surface Growth mode, low seed concentration is used to promote the rate of deposition, which expands the ridge–valley competition favoring growth at the active sites. The understanding and rational control of the chiral ridges will advance the synthetic control for chiral nanostructures. [ABSTRACT FROM AUTHOR]

Molecular metal oxo or oxo/alkoxo clusters, MwOx(OH/OR)y(L/X)z (L or X = organic ligands), can often be isolated upon (partial) hydrolysis of metal alkoxides. Investigation of such clusters leads to a better understanding of the basic processes of sol–gel chemistry. The ligands not only stabilize the cluster core but also influence to some extent the cluster structures. They can easily change their position on the cluster surface, thus adapting to changing cluster geometries, and can be exchanged under certain conditions. A close inspection of titanium oxo/alkoxo cluster structures, taken as an informative example, shows that Ti3O units (with or without organic ligands) are the basic building blocks. Clusters with higher nuclearities appear to be predominantly formed by cluster–cluster or by cluster–monomer condensations. Ligand substitution or condensation reactions within a cluster unit are also possible. Highlights: Comparison of metal oxo cluster structures allows conclusions on the mechanisms by which the clusters might be formed or modified. Organic ligands protecting the cluster core are dynamic and can be exchanged. Organic ligands influence the cluster structure. Ti3O units are the basic building blocks in titanium oxo clusters. [ABSTRACT FROM AUTHOR]

Carbon monoxide has been recognized relatively recently as signaling molecule, and only very few dedicated natural CO sensor proteins have been identified so far. These include in particular heme-based transcription factors: the bacterial sensor proteins CooA and RcoM. In these 6-coordinated systems, exchange between an internal protein residue and CO as a heme ligand in the sensor domain affects the properties of the DNA-binding domain. Using light to dissociate heme-ligand bonds can in principle initiate this switching process. We review the efforts to use this method to investigate early processes in ligand switching and signaling, with an emphasis on the CO-“trappingˮ properties of the heme cavity. These features are unusual for most heme proteins, but common for heme-based CO sensors.

The dynamic interactions of enzymes and substrates underpins catalysis, yet few techniques can interrogate the dynamics of protein-bound ligands. Here we describe the use of field cycling NMR relaxometry to measure the dynamics of enzyme-bound substrates and cofactors in catalytically competent complexes of GMP reductase. These studies reveal new binding modes unanticipated by x-ray crystal structures and reaction-specific dynamic networks. Importantly, this work demonstrates that distal interactions not usually considered part of the reaction coordinate can play an active role in catalysis. The commercialization of shuttling apparatus will make field cycling relaxometry more accessible and expand its use to additional nuclei, promising more intriguing findings to come.

Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein–ligand structures, X‐ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein–ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron‐density maps are comparable and Rfree values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular‐dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non‐unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail. [ABSTRACT FROM AUTHOR]

• Photoreactions of alkenyl- and thiolate-bridged diiron carbonyls with alkynes. • A series of thiolate-bridged diiron acyl complexes was synthesized. • Facile insertion of alkynes into the iron-alkenyl bond is followed by CO insertion. • Dynamic behavior of an alkenyl-thiolate ligand was investigated. The alkenyl- and thiolate-bridged diiron carbonyl complexes [Fe 2 (μ-SC 6 H 4 CR1CH)(CO) 6 ] (R1 = H or Me), which are derived from [Fe 3 (CO) 12 ] and benzothiophenes, reacted with alkynes (R2CCR3) under photoirradiation conditions to form the acyl complexes [Fe 2 {μ-SC 6 H 4 CR1CHCR2C(R3)CO}(CO) 5 ]. In this reaction, an alkyne and CO are inserted into the Fe–alkenyl bond, and the bulky substituents of alkynes, including a redox active ferrocenyl group, occupy the R3 position. To elucidate the reaction pathway, the reaction of the in situ generated acetonitrile complex [Fe 2 (μ-SC 6 H 4 CHCH)(CO) 5 (NCCH 3)] with ethynylbenzene was monitored by 1H NMR spectroscopy. The results demonstrated that the acetonitrile complex undergoes facile insertion of the alkyne, which is followed by CO insertion to give the corresponding acyl complex [Fe 2 {μ-SC 6 H 4 (CH) 3 C(Ph)CO}(CO) 5 ]. The reactivity of the bridging alkenyl moiety is related to the dynamic behavior of the alkenyl-thiolate ligand (SC 6 H 4 CHCH)2- as well as the entering alkyne. Temperature dependent 31P NMR measurements of the dmpm-bridged complex [Fe 2 (μ-SC 6 H 4 CHCH)(μ-dmpm)(CO) 4 ] (dmpm = bis(dimethylphosphino)methane) revealed that the activation parameters for the flip-flop motion of the alkenyl-thiolate ligand are Δ H ‡ = 46.7(7) kJ mol-1 and Δ S ‡ = −46(2) J mol-1 K-1. [Display omitted] [ABSTRACT FROM AUTHOR]

Clusters can be model systems for nanoparticles with regard to the chemistry of surface groups. Metal oxo clusters with carboxylato ligands are easily accessible and therefore well-suited for investigating the chemistry of cluster-bonded ligands. This review article gives an account on issues like ligand dynamics, post-synthesis ligand exchange, stability of the cluster core during ligand exchange, possible mechanisms of intra- and intermolecular ligand exchange or utilizing functional ligands. [ABSTRACT FROM AUTHOR]

The interfacial adsorption, desorption, and exchange behaviors of thiolated ligands on nanotextured Au nanoparticle surfaces exhibit phenomenal site-to-site variations essentially dictated by the local surface curvatures, resulting in heterogeneous thermodynamic and kinetic profiles remarkably more sophisticated than those associated with the self-assembly of organothiol ligand monolayers on atomically flat Au surfaces. Here we use plasmon-enhanced Raman scattering as a spectroscopic tool combining time-resolving and molecular fingerprinting capabilities to quantitatively correlate the ligand dynamics with detailed molecular structures in real time under a diverse set of ligand adsorption, desorption, and exchange conditions at both equilibrium and nonequilibrium states, which enables us to delineate the effects of nanoscale surface curvature on the binding affinity, cooperativity, structural ordering, and the adsorption/desorption/exchange kinetics of organothiol ligands on colloidal Au nanoparticles. This work provides mechanistic insights on the key thermodynamic, kinetic, and geometric factors underpinning the surface curvature-dependent interfacial ligand behaviors, which serve as a central knowledge framework guiding the site-selective incorporation of desired surface functionalities into individual metallic nanoparticles for specific applications. [ABSTRACT FROM AUTHOR]

A series of new chiral [(NHC)Au(I)Cl] are synthesized. The chiral NHC ligands feature pairs of ortho-biphenyl groups. The distal phenyl groups of the biphenyl substituents are varied from simple phenyl, 3,5-dimethylphenyl, to 3,5-di-t-butylphenyl. X-Ray structure analysis were performed for two such [(NHC)Au(I)Cl] complexes. High percent buried volumes were calculated for two novel chiral [(NHC)Au(I)Cl]complexes whose structure were solved by an X-ray analysis. The rotational motion in the biphenyl group is slow on the NMR time scale. Rotational barriers were determined using WINDNMR for two of the chiral gold complexes. [ABSTRACT FROM AUTHOR]

Background The nature of ligand motion in proteins is difficult to characterize directly usingexperiment. Specifically, it is unclear to what degree these motions are coupled. Methods All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. Results Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. Conclusions Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. General significance Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics. [ABSTRACT FROM AUTHOR]

The catalytic site of heme–copper oxidases encompasses two close-lying ligand binding sites: the heme, where oxygen is bound and reduced and the Cu B atom, which acts as ligand entry and release port. Diatomic gaseous ligands with a dipole moment, such as the signaling molecules carbon monoxide (CO) and nitric oxide (NO), carry clear infrared spectroscopic signatures in the different states that allow characterization of the dynamics of ligand transfer within, into and out of the active site using time-resolved infrared spectroscopy. We review the nature and diversity of these processes that have in particular been characterized with CO as ligand and which take place on time scales ranging from femtoseconds to milliseconds. These studies have advanced our understanding of the functional ligand pathways and reactivity in enzymes and more globally represent intriguing model systems for mechanisms of ligand motion in a confined protein environment. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems. [ABSTRACT FROM AUTHOR]

Carbon monoxide has been recognized relatively recently as signaling molecule, and only very few dedicated natural CO sensor proteins have been identified so far. These include in particular heme-based transcription factors: the bacterial sensor proteins CooA and RcoM. In these 6-coordinated systems, exchange between an internal protein residue and CO as a heme ligand in the sensor domain affects the properties of the DNA-binding domain. Using light to dissociate heme-ligand bonds can in principle initiate this switching process. We review the efforts to use this method to investigate early processes in ligand switching and signaling, with an emphasis on the CO-"trappingˮ properties of the heme cavity. These features are unusual for most heme proteins, but common for heme-based CO sensors., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Vos, Salman and Liebl.)

The dynamic behavior of the N, N, N′, N′-tetramethylethylenediamine (tmeda) ligand has been studied in solid lithium-fluorenide(tmeda) ( 3) and lithium-benzo[ b]fluorenide(tmeda) ( 4) using CP/MAS solid-state 13C- and 15N-NMR spectroscopy. It is shown that, in the ground state, the tmeda ligand is oriented parallel to the long molecular axis of the fluorenide and benzo[ b]fluorenide systems. At low temperature (<250 K), the 13C-NMR spectrum exhibits two MeN signals. A dynamic process, assigned to a 180° rotation of the five-membered metallacycle ( π-flip), leads at elevated temperatures to coalescence of these signals. Line-shape calculations yield Δ H‡=42.7 kJ mol−1, Δ S‡=−5.3 J mol−1 K−1, and $\rm{\Delta G_{298}^{\ddag}}$=44.3 kJ mol−1 for 3, and Δ H‡=36.8 kJ mol−1, Δ S‡=−17.7 J mol−1 K−1, and $\rm{\Delta G_{298}^{\ddag}}$=42.1 kJ mol−1 for 4, respectively. A second dynamic process, assigned to ring inversion of the tmeda ligand, was detected from the temperature dependence of T1 ρ, the 13C spin-lattice relaxation time in the rotating frame, and led to Δ H‡=24.8 kJ mol−1, Δ S‡=−49.2 J mol−1 K−1, and $\rm{\Delta G_{298}^{\ddag}}$=39.5 kJ mol−1 for 3, and Δ H‡=18.2 kJ mol−1, Δ S‡=−65.3 J mol−1 K−1, and $\rm{\Delta G_{298}^{\ddag}}$=37.7 kJ mol−1 for 4, respectively. For (D12)- 3, the rotation of the CD3 groups has also been studied, and a barrier Ea of 14.1 kJ mol−1 was found. [ABSTRACT FROM AUTHOR]

Abstract: Optical spectroscopy on ensembles and single CdSe/ZnS semiconductor quantum dots (QDs) demonstrates a competition of trap and near band edge photoluminescence (PL). This competition can be markedly influenced by a few surface attached pyridyl functionalized dye molecules (porphyrins or perylene diimides) forming nanoassemblies with well defined geometries. Temperature variation and related changes in absorption and emission reveal sharp changes of the ligand shell structure in a narrow temperature range for organic (TOPO and amine) surfactants (phase transition). The effects on QD PL at this transition become considerably pronounced upon attachment of only a few dye molecules to QD surface. Moreover, under ambient conditions amine capped QDs are photodegraded in the course of time. This process is enhanced by attached dye molecules both on the ensemble and single particle/dye level. This investigation elaborates the importance of (switchable) surface states for the characterization of the PL of QDs. [Copyright &y& Elsevier]

Pin1 is a modular enzyme that accelerates the cis-trans isomerization of phosphorylated-Ser/Thr-Pro (pS/T-P) motifs found in numerous signaling proteins regulating cell growth and neuronal survival. We have used NMR to investigate the interaction of Pin1 with three related ligands that include a pS-P substrate peptide, and two pS-P substrate analogue inhibitors locked in the cis and trans conformations. Specifically, we compared the ligand binding modes and binding-induced changes in Pin1 side-chain flexibility. The cis and trans binding modes differ, and produce different mobility in Pin1. The cis-locked inhibitor and substrate produced a loss of side-chain flexibility along an internal conduit of conserved hydrophobic residues, connecting the domain interface with the isomerase active site. The trans-locked inhibitor produces a weaker conduit response. Thus, the conduit response is stereoselective. We further show interactions between the peptidyl-prolyl isomerase and Trp-Trp (WW) domains amplify the conduit response, and alter binding properties at the remote peptidyl-prolyl isomerase active site. These results suggest that specific input conformations can gate dynamic changes that support intraprotein communication. Such gating may help control the propagation of chemical signals by Pin1, and other modular signaling proteins. [ABSTRACT FROM AUTHOR]

Abstract: The active site of nitric oxide reductase from Paracoccus denitrificans contains heme and non-heme iron and is evolutionarily related to heme-copper oxidases. The CO and NO dynamics in the active site were investigated using ultrafast transient absorption spectroscopy. We find that, upon photodissociation from the active site heme, 20% of the CO rebinds in 170 ps, suggesting that not all the CO transiently binds to the non-heme iron. The remaining 80% does not rebind within 4 ns and likely migrates out of the active site without transient binding to the non-heme iron. Rebinding of NO to ferrous heme takes place in ~13 ps. Our results reveal that heme-ligand recombination in this enzyme is considerably faster than in heme-copper oxidases and are consistent with a more confined configuration of the active site. [Copyright &y& Elsevier]

The dynamic interactions of enzymes and substrates underpins catalysis, yet few techniques can interrogate the dynamics of protein-bound ligands. Here we describe the use of field cycling NMR relaxometry to measure the dynamics of enzyme-bound substrates and cofactors in catalytically competent complexes of GMP reductase. These studies reveal new binding modes unanticipated by x-ray crystal structures and reaction-specific dynamic networks. Importantly, this work demonstrates that distal interactions not usually considered part of the reaction coordinate can play an active role in catalysis. The commercialization of shuttling apparatus will make field cycling relaxometry more accessible and expand its use to additional nuclei, promising more intriguing findings to come., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Roberts and Hedstrom.)

Nanocrystal surfaces are commonly populated by organic ligands, which play a determining role in the optical, electronic, thermal, and catalytic properties of the individual nanocrystals and their assemblies. Understanding the bonding of ligands to nanocrystal surfaces and their dynamics is therefore important for the optimization of nanocrystals for different applications. In this study, we use temperature-dependent, quasi-elastic neutron scattering (QENS) to investigate the dynamics of different surface bound alkanethiols in lead sulfide nanocrystal solids. We select alkanethiols with mono- and dithiol terminations, as well as different backbone types and lengths. QENS spectra are collected both on a time-of-flight spectrometer and on a backscattering spectrometer, allowing us to investigate ligand dynamics in a time range from a few picoseconds to nanoseconds. Through model-based analysis of the QENS data, we find that ligands can either (1) precess around a central axis, while simultaneously rotating around their own molecular axis, or (2) only undergo uniaxial rotation with no precession. We establish the percentage of ligands undergoing each type of motion, the average relaxation times, and activation energies for these motions. We determine, for example, that dithiols which link facets of neighboring nanocrystals only exhibit uniaxial rotation and that longer ligands have higher activation energies and show smaller opening angles of precession due to stronger ligand-ligand interactions. Generally, this work provides insight into the arrangement and dynamics of ligands in nanocrystal solids, which is key to understanding their mechanical and thermal properties, and, more generally, highlights the potential of QENS for studying ligand behavior.

Surface ligand dynamics of colloidal quantum dots (QDs) has been revealed as an important issue for determining QDs performance in their synthesis and postsynthesis treatment, such as ligand-related photoluminescence, colloidal stability, and so forth. However, this issue is less associated with the preparation of highly luminescent nanocomposites, which usually leads to poor performance and repeatability. In this work, on the basis of the studies about surface ligand dynamics of aqueous QDs, highly luminescent QDs-cellulose composites are prepared and employed to fabricate high color purity light-emitting diodes (LEDs). Detailed investigations indicate that the species of QD capping ligands and in particular the temperature are the key for controlling the ligand dynamics. The preparation of nanocomposites using less dynamic ligand-modified QDs at low temperature overcomes the conventional problems of QD aggregation, low QD content, luminescence quenching and shift, thus producing highly luminescent QDs-cellulose composites. This protocol is available for a variety of aqueous QDs, such as CdS, CdSe, CdTe, and CdSe(x)Te(1-x), which permits the design and fabrication of QD-based LEDs using the nanocomposites as color conversion layer on a blue emitting InGaN chip.