Single Atom Substitution Research Articles

Structural Basis for Aza-Glycine Stabilization of Collagen.

Previously, we have demonstrated that replacement of the strictly conserved glycine in collagen with aza-glycine provides a general solution for stabilizing triple helical collagen peptides (Chenoweth, D. M.; et al. J. Am. Chem. Soc. 2016, 138, 9751 ; 2015, 137, 12422 ). The additional hydrogen bond and conformational constraints provided by aza-glycine increases the thermal stability and rate of folding in collagen peptides composed of Pro-Hyp-Gly triplet repeats, allowing for truncation to the smallest self-assembling peptide systems observed to date. Here we show that aza-glycine substitution enhances the stability of an arginine-containing collagen peptide and provide a structural basis for this stabilization with an atomic resolution crystal structure. These results demonstrate that a single nitrogen atom substitution for a glycine alpha-carbon increases the peptide's triple helix melting temperature by 8.6 °C. Furthermore, we provide the first structural basis for stabilization of triple helical collagen peptides containing aza-glycine and we demonstrate that minimal alteration to the peptide backbone conformation occurs with aza-glycine incorporation.

Suppressing Isomerization of Phosphine-Protected Au9 Cluster by Bond Stiffening Induced by a Single Pd Atom Substitution.

The fluxional nature of small gold clusters has been exemplified by reversible isomerization between [Au9(PPh3)8]3+ with a crown motif (Au9(C)) and that with a butterfly motif (Au9(B)) induced by association and dissociation with compact counteranions (NO3-, Cl-). However, structural isomerization was suppressed by substitution of the central Au atom of the Au9 core in [Au9(PPh3)8]3+ with a Pd atom: [PdAu8(PPh3)8]2+ with a crown motif (PdAu8(C)) did not isomerize to that with a butterfly motif (PdAu8(B)) upon association with the counteranions. Density functional theory calculation showed that the energy difference between PdAu8(C) and PdAu8(B) is comparable to that between Au9(C) and Au9(B), indicating that the relative stabilities of the isomers are not a direct cause for the suppression of isomerization. Temperature dependence of Debye-Waller factors obtained by X-ray absorption fine-structure analysis revealed that the intracluster bonds of PdAu8(C) were stiffer than the corresponding bonds in Au9(C). Natural bond orbital analysis suggested that the radial Pd-Au and lateral Au-Au bonds in PdAu8(C) are stiffened due to the increase in the ionic nature and decrease in electrostatic repulsion between the surface Au atoms, respectively. We conclude that the formation of stiffer metal-metal bonds by Pd atom doping inhibits the isomerization from PdAu8(C) to PdAu8(B).

2-Thiouracil intersystem crossing photodynamics studied by wavelength-dependent photoelectron and transient absorption spectroscopies.

Single-atom substitution within a natural nucleobase-such as replacing oxygen by sulfur in uracil-can result in drastic changes in the relaxation dynamics after UV excitation. While the photodynamics of natural nucleobases like uracil are dominated by pathways along singlet excited states, the photodynamics of thiobases like 2-thiouracil populate the triplet manifold with near unity quantum yield. In the present study, a synergistic approach based on time-resolved photoelectron spectroscopy (TRPES), time-resolved absorption spectroscopy (TRAS), and ab initio computations has been particularly successful at unraveling the underlying photophysical principles and describing the dissimilarities between the natural and substituted nucleobases. Specifically, we find that varying the excitation wavelength leads to differences between gas-phase and condensed-phase experimental results. Systematic trends are observed in the intersystem crossing time constants with varying excitation wavelength, which can be readily interpreted in the context of ab initio calculations performed both in vacuum and including solvent effects. Thus, the combination of TRPES and TRAS experiments with high-level computational techniques allows us to characterize the topology of the potential energy surfaces defining the relaxation dynamics of 2-thiouracil in both gas and condensed phases, as well as investigate the accessibility of conical intersections and crossings, and potential energy barriers along the associated relaxation coordinates.

The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts

Thioamides are single atom substitutions of the peptide bond that serve as versatile probes of protein structure. Effective use of thioamides requires a robust understanding of the impact that the substitution has on a protein of interest. However, the thermodynamic effects of thioamide incorporation have only been studied in small structural motifs, and their influence on secondary structure in the context of full-length proteins is not known. Here we describe a comprehensive survey of thioamide substitutions in three benchmark protein systems (calmodulin, the B1 domain of protein G, and collagen) featuring the most prevalent secondary structure motifs: α-helix, β-sheet, and polyproline type II helix. We find that in most cases, effects on thermostability can be understood in terms of the positioning and local environment of the thioamide relative to proximal structural elements and hydrogen bonding networks. These observations set the stage for the rational design of thioamide substituted proteins with predictable stabilities.

Upgrading Electroresistive Memory from Binary to Ternary Through Single-Atom Substitution in the Molecular Design.

Herein, two molecules based on urea and thiourea, which differ by only a single atom, were designed, successfully synthesized, and fabricated into resistive random-access memory devices (RRAM). The urea-based molecule showed binary write-once-read-many (WORM) storage behavior, whereas the thiourea-based molecule demonstrated ternary storage behavior. Atomic-force microscopy (AFM) and X-ray diffraction (XRD) patterns show that both molecules have smooth morphology and ordered layer-by-layer lamellar packing, which is beneficial for charge transportation and, consequently, device performance. Additionally, the optical and electrochemical properties indicate that the thiourea-based molecule has a lower bandgap and may be polarized by trapped charges, thus the formation of a continuous conductive channel and electric switching occurs at lower bias voltage, which results in ternary WORM behavior. This study, together with our previous work on single-atom substitution, may be useful to tune and improve device performance in the future design of organic memory.

Thioxylated cyclosporin A for studying protein–drug interactions

Single atom substitution of cyclosporin A (CsA) through thioxylation has been used to study the structure–activity relationship of the immunosuppressive complex, involving the CsA receptor protein cyclophilin 18 (Cyp18) and the immunological target protein phosphatase calcineurin (CaN), illustrating the contributions of peptide backbone in protein–drug interaction. Moreover, the subtle difference between thioxylation positions in CsA has led to a remarkable change in the quenching effect on Cyp18 intrinsic fluorescence. Using the thioxylated compound Cs7 as an isosteric derivative of CsA in competition assay, the experiment has led to the determination of koff value in solution. Whereas the conformational heterogeneity of CsA has been found to be associated with its two-phase binding kinetics to Cyp18, the dissociation rate of CsA from complex is independent from the initial ligand structure.

Widespread Perturbation of Function, Structure, and Dynamics by a Conservative Single-Atom Substitution in Thymidylate Synthase.

Thymidylate synthase (TSase) is responsible for synthesizing the sole de novo source of dTMP in all organisms. TSase is a drug target, and as such, it has been well studied in terms of both structure and reaction mechanism. Cysteine 146 in Escherichia coli TSase is universally conserved because it serves as the nucleophile in the enzyme mechanism. Here we use the C146S mutation to probe the role of the sulfur atom in early events in the catalytic cycle beyond serving as the nucleophile. Surprisingly, the single-atom substitution severely decreases substrate binding affinity, and the unfavorable ΔΔG°bind is comprised of roughly equal enthalpic and entropic components at 25 °C. Chemical shifts in the free and dUMP-bound states show the mutation causes perturbations throughout TSase, including regions important for complex stability, in agreement with a less favorable enthalpy change. We measured the nuclear magnetic resonance methyl symmetry axis order parameter (S2axis), a proxy for conformational entropy, for TSase at all vertices of the dUMP binding/C146S mutation thermodynamic cycle and found that the calculated TΔΔS°conf is similar in sign and magnitude to the calorimetric TΔΔS°. Further, we ascribed minor resonances in wild-type-dUMP spectra to a state with a covalent bond between Sγ of C146 and C6 of dUMP and find S2axis values are unaffected by covalent bond formation, indicating this reaction step is neutral with respect to ΔS°conf. Lastly, the C146S mutation allowed us to measure cofactor analog binding by isothermal titration calorimetry without the confounding heat signature of covalent bond formation. Raltitrexed binds free and singly bound TSase with similar affinities, yet the two binding events have different enthalpy changes, providing further evidence of communication between the two active sites.

ChemInform Abstract: Pathways for Oxygen‐Isotope Exchange in Two Model Oxide Clusters

AbstractReview: 35 refs.

Impurity effects on solid-solid transitions in atomic clusters.

We use the harmonic superposition approach to examine how a single atom substitution affects low-temperature anomalies in the vibrational heat capacity (CV) of model nanoclusters. Each anomaly is linked to competing solidlike "phases", where crossover of the corresponding free energies defines a solid-solid transition temperature (Ts). For selected Lennard-Jones clusters we show that Ts and the corresponding CV peak can be tuned over a wide range by varying the relative atomic size and binding strength of the impurity, but excessive atom-size mismatch can destroy a transition and may produce another. In some tunable cases we find up to two additional CV peaks emerging below Ts, signalling one- or two-step delocalisation of the impurity within the ground-state geometry. Results for Ni74X and Au54X clusters (X = Au, Ag, Al, Cu, Ni, Pd, Pt, Pb), modelled by the many-body Gupta potential, further corroborate the possibility of tuning, engineering, and suppressing finite-system analogues of a solid-solid transition in nanoalloys.

Widespread Perturbation of Function, Structure, and Dynamics by a Conservative Single-Atom Substitution in Thymidylate Synthase

Widespread Perturbation of Function, Structure, and Dynamics by a Conservative Single-Atom Substitution in Thymidylate Synthase

M3Ag17(SPh)12 Nanoparticles and Their Structure Prediction.

Although silver nanoparticles are of great fundamental and practical interest, only one structure has been determined thus far: M4Ag44(SPh)30, where M is a monocation, and SPh is an aromatic thiolate ligand. This is in part due to the fact that no other molecular silver nanoparticles have been synthesized with aromatic thiolate ligands. Here we report the synthesis of M3Ag17(4-tert-butylbenzene-thiol)12, which has good stability and an unusual optical spectrum. We also present a rational strategy for predicting the structure of this molecule. First-principles calculations support the structural model, predict a HOMO-LUMO energy gap of 1.77 eV, and predict a new "monomer mount" capping motif, Ag(SR)3, for Ag nanoparticles. The calculated optical absorption spectrum is in good correspondence with the measured spectrum. Heteroatom substitution was also used as a structural probe. First-principles calculations based on the structural model predicted a strong preference for a single Au atom substitution in agreement with experiment.

Structural Models of Poly(cyclopentadithiophene-alt-benzothiadiazole) with Branched Side Chains: Impact of a Single Fluorine Atom on the Crystal Structure and Polymorphism of a Conjugated Polymer

This study describes the impact of a single fluorine atom substitution in the conjugated backbone of poly(cyclopentadithiophene-alt-benzothiadiazole) on the structure and the polymorphism of the polymer bearing 2-ethylhexyl side chains. Controlled growth of the nonfluorinated and fluorinated polymers by solvent vapor annealing (SVA), melt-crystallization on oriented poly(tetrafluoroethylene), and high-temperature rubbing yield highly crystalline and/or oriented films of a thermodynamically stable polymorph called form I. The single-crystal hk0 and the oriented fiber patterns are obtained in films prepared by SVA and aligned films, respectively. Form I involves a high-symmetry packing of four chains in an orthorhombic cell (Pccn space group) with pseudohexagonal symmetry. The chains are paired into dimers with a 3.6–3.8 A interchain π-stacking distance and a segregated mode of stacking of cyclopentadithiophene and benzothiadiazole (BT). A single H/F substitution on the BT unit modifies the orientation of t...

Carbon Doping in Boron Suboxide: Structure, Energetics, and Elastic Properties

The structural, electronic, and elastic properties of pristine and carbon‐doped boron suboxide (B6O) are calculated using density functional theory. The results indicate that it is energetically preferable for a single carbon atom to substitute into an oxygen site rather than a boron site. The lattice parameters and cell volume increase to relieve the residual stress created by the carbon substitution. The interstitial position is not favorable for a single atom substitution. However, if two carbon atoms substitute for two neighboring oxygen atoms, then it becomes energetically favorable to dope an interstitial oxygen, boron, or carbon atom along the C–C chain. If the interstitial dopant is either boron or carbon, a local B4C‐like structure with either a C–B–C or C–C–C chain is created within the boron suboxide unit cell. The resulting structure shows improvements in the bulk modulus at the expense of the shear and Young's moduli. The moduli further improve if an additional carbon is substituted within a polar or equatorial site of the neighboring B12 icosahedron. Based on these calculations, we conclude that carbon doping can either harden or soften B6O depending on the manner in which the substitutions are populated. Furthermore, as B6O samples are often oxygen deficient, C doping can occupy such sites and improve the elastic properties.

Replacing uridine with 2-thiouridine enhances the rate and fidelity of nonenzymatic RNA primer extension.

The nonenzymatic replication of RNA oligonucleotides is thought to have played a key role in the origin of life prior to the evolution of ribozyme-catalyzed RNA replication. Although the copying of oligo-C templates by 2-methylimidazole-activated G monomers can be quite efficient, the copying of mixed sequence templates, especially those containing A and U, is particularly slow and error-prone. The greater thermodynamic stability of the 2-thio-U(s2U):A base pair, relative to the canonical U:A base pair, suggests that replacing U with s2U might enhance the rate and fidelity of the nonenzymatic copying of RNA templates. Here we report that this single atom substitution in the activated monomer improves both the kinetics and the fidelity of nonenzymatic primer extension on mixed-sequence RNA templates. In addition, the mean lengths of primer extension products obtained with s2U is greater than those obtained with U, augmenting the potential for nonenzymatic replication of heritable function-rich sequences. We suggest that noncanonical nucleotides such as s2U may have played a role during the infancy of the RNA world by facilitating the nonenzymatic replication of genomic RNA oligonucleotides.

Characterizing RNA Excited States Using NMR Relaxation Dispersion.

Changes in RNA secondary structure play fundamental roles in the cellular functions of a growing number of noncoding RNAs. This chapter describes NMR-based approaches for characterizing microsecond-to-millisecond changes in RNA secondary structure that are directed toward short-lived and low-populated species often referred to as "excited states." Compared to larger scale changes in RNA secondary structure, transitions toward excited states do not require assistance from chaperones, are often orders of magnitude faster, and are localized to a small number of nearby base pairs in and around noncanonical motifs. Here, we describe a procedure for characterizing RNA excited states using off-resonance R1ρ NMR relaxation dispersion utilizing low-to-high spin-lock fields (25-3000 Hz). R1ρ NMR relaxation dispersion experiments are used to measure carbon and nitrogen chemical shifts in base and sugar moieties of the excited state. The chemical shift data are then interpreted with the aid of secondary structure prediction to infer potential excited states that feature alternative secondary structures. Candidate structures are then tested by using mutations, single-atom substitutions, or by changing physiochemical conditions, such as pH and temperature, to either stabilize or destabilize the candidate excited state. The resulting chemical shifts of the mutants or under different physiochemical conditions are then compared to those of the ground and excited states. Application is illustrated with a focus on the transactivation response element from the human immune deficiency virus type 1, which exists in dynamic equilibrium with at least two distinct excited states.

Effect of single atom substitution in benzochalcogendiazole acceptors on the performance of ternary memory devices

Ternary memory storage performances of three benzochalcogendiazole derivative based devices clearly demonstrate the effect of single atom substitution on the molecular planarity, film morphologies and device threshold voltages.

Triggering DRAM/SRAM memory behaviors by single atom substitution to alter the molecular planarity

A novelty: achieving different types of memory devices through single atom substitution to alter the molecular planarity thus improves the intramolecular dihedral angle.

Dithioamide Peptides and Proteins: Synthesis and Application to Tracking Protein Conformational Changes by Fluorescence Spectroscopy

Tracking protein conformational change is important to understand the folding and function of proteins. Forster resonant energy transfer (FRET) and photo-induced electron transfer (PET) are widely used to get time-resolved structural information on protein motions. However, the relatively large size of fluorophores and quenchers may introduce significant perturbations to protein structure. The thioamide bond, a single atom substitution of the peptide bond, has recently been shown to be a minimalist fluorescent quencher of various fluorophores by either FRET- or PET- based mechanisms. Unlike commonly used fluorescence probes, thioamides are sufficiently small that they can be placed at nearly any position in the protein sequence without significant alteration of the secondary structure. However, moderate quenching efficiency may limit its sensitivity for some applications. Here, we show that two consecutive thioamide bonds can be incorporated into peptide and protein backbones, and the quenching effect is strengthened compared with a mono-thioamide. Thus dithioamide bonds provide increased sensitivity to detect protein conformational changes and may be used for advanced spectroscopy applications like Fluorescence correlation spectroscopy (FCS) and Fluorescence lifetime imaging microscopy (FLIM).

Theoretical and computational investigation of meta-phenylene as ferromagnetic coupler in nitronyl nitroxide diradicals

We predict the magnetic exchange coupling constant (J) for 27 m-phenylene-based nitronyl nitroxide (NN) diradicals with nine different substituents in three unique (common ortho, ortho–meta and common meta) positions on the coupler unit by using the broken-symmetry density functional methodology. For all investigated diradicals, J values are computed using B3LYP, B3LYP-D3 and M06-2X functionals with 6–311+G(d,p) basis set. The JM06-2X value is larger than JB3LYP and closer to the observed value for the unsubstituted species. Substitutions at common ortho position always produce a greater angle of twist between the spin source and the coupler units. When the twist angle is very large, the nature of intramolecular magnetic interaction changes from ferromagnetic to antiferromagnetic. In these cases, the coupler–NN bond order becomes small. Substitution at the common meta position of m-phenylene in the diradical has little steric and hydrogen-bonding effects. Electron-withdrawing groups reveal a specific trend for single-atom substitution. An ortho substitution generally decreases J and a meta substitution always increases J with a decreasing −I effect. Variation of J with planarity as well as Hammett constant is investigated. The nucleus-independent chemical shift value is found to decrease from the corresponding mono-substituted phenyl derivatives. The dependence of J on these factors is explored.

Isomorphous substituted bimetallic oxide cluster as a novel strategy for single-atom catalysis

Single-atom catalysis of isomorphous substituted bimetallic oxide TMV3O10 (TM=Sc, Ti, Cr and Co) is explored by spin–polarized density functional theory calculations. The single atom substitution in V4O10 does not make significant change to the geometric or electronic structures of the cluster; while it brings specific and tunable catalytic activity depending on the TM substituent. The d-projected density of state near the Fermi level is found to play important roles in the catalytic performance of single-atom catalysts. Our findings reveal the structural basis of the activity of bimetallic oxide clusters and shed some lights on the catalytic mechanism of single-atom catalysis.