Bridging Solvent Research Articles

Time-resolved keto-enol tautomerization of the medicinal pigment curcumin.

Curcumin is a medicinal agent that exhibits anti-cancer and anti-Alzheimer's disease properties. It has a keto-enol moiety that gives rise to many of its chemical properties including metal complexation and acid-base equilibria. A previous study has shown that keto-enol tautomerization at this moiety is implicated in the anti-Alzheimer's disease effect of curcumin, highlighting the importance of this process. In this study, tautomerization of curcumin in methanol, acetone and acetonitrile was investigated using time-resolved 1H nuclear magnetic resonance spectroscopy. Curcumin undergoes hydrogen-deuterium exchange with the solvents and the proton resonance peak corresponding to the hydrogen at the α-carbon position (Cα) decays as a function of time, signifying deuteration at this position. Because tautomerization is the rate limiting step in the deuteration of curcumin at the Cα position, the rate of tautomerization is inferred from the rate of deuteration. The rate constant of tautomerization of curcumin shows a temperature dependence and analysis using the Arrhenius equation revealed activation energies (Ea) of tautomerization of (80.1 ± 5.9), (64.1 ± 1.0) and (68.3 ± 5.5) kJ mol-1 in methanol, D2O/acetone and D2O/acetonitrile, respectively. Insight into the role of water in tautomerization of curcumin was further offered by density functional theory studies. The transition state of tautomerization was optimized in the presence of water molecules. The results show a hydrogen-bonded solvent bridge between the diketo moiety and Cα of curcumin. The Ea of tautomerization of curcumin shows a strong dependence on the number of water molecules in the solvent bridge, indicating the critical role played by the solvent bridge in catalyzing tautomerization of curcumin.

High-yield synthesis of 2,5-Furandicarboxylic acid from fructose via a two-step strategy without 5-Hydroxymethylfurfural isolation using dioxane as a bridging solvent

2,5-Furandicarboxylic acid (FDCA) is a crucial bio-platform molecule for renewable polymers and fine chemicals. Here, a two-step method including fructose dehydration and 5-hydroxymethylfurfural (HMF) oxidation has been reported as an effective strategy to produce FDCA with high yield from fructose directly. In this method, for fructose dehydration over CH3SO3H, tetramethylammonium chloride (TmaCl) was first used as phase modifier and co-solvent in a H2O-dioxane biphasic-solvent system, affording HMF yield up to 90.6 % under mild condition (383 K) with relatively high fructose concentration (e.g. 5–10 wt %). Detailed 13C NMR studies verified the interaction between TmaCl and fructose, which significantly promoted the proportion of fructofuranoses and helped to improve the fructose dehydration activity and HMF yield. After dehydration step, more than 97.8 % of CH3SO3H were recovered in reaction phase for catalyst reuse, while the dioxane solution of extracted HMF was separated via simple phase separation. Followed by water commixing, this HMF dioxane solution (with the HMF concentration of 6.3 wt %) was directly oxidized over Ru/C (393 K, 1 MPa O2) to produce FDCA without HMF isolation and alkali addition, affording FDCA yield near 90 %. This study integrates the fructose dehydration and HMF oxidation rationally via dioxane as the bridging solvent to achieve high FDCA yield without complex HMF purification steps, and thus proposes an applicable model for high-efficient production of FDCA in practice.

Effect of Hydrophobic Moieties on the Assembly of Silica Particles into Colloidal Crystals

To boost the implementation of colloidal crystals (CCs) in separation science, the effects of the most common chromatographic reversed phases, that is, butyl and octadecyl, on the assembly of silica particles into CCs and on the optical properties of CCs are investigated. Interestingly, particle surface modification can cause phase separation during sedimentation because the assembly is highly sensitive to minute changes in surface characteristics. Solvent-induced surface charge generation through acid-base interactions of acidic residual silanol groups with the solvent is enough to promote colloidal crystallization of modified silica particles. In addition, solvation forces at small interparticle distances are also involved in colloidal assembly. The characterization of CCs formed during sedimentation or via evaporative assembly revealed that C4 particles can form CCs more easily than C18 particles because of their low hydrophobicity; the latter can only form CCs in tetrahydrofuran when C18 chains with a high bonding density have extra hydroxyl side groups. These groups can only be hydrolyzed from trifunctional octadecyl silane but not from a monofunctional one. Moreover, after evaporative assembly, CCs formed from particles with different surface moieties exhibit different lattice spacings because their surface hydrophobicity and chemical heterogeneity can modulate interparticle interactions during the two main stages of assembly: the wet stage of crystal growth and the late stage of nano dewetting (evaporation of interparticle solvent bridges). Finally, short, alkyl-modified CCs were effectively assembled inside silica capillaries with a 100 μm inner diameter, laying the foundation for future chromatographic separation using capillary columns.

Characterization and investigation of intermediate stages during anion-exchange reaction between CsPbBr3 and CsPbI3 nanocrystal solution and film via photoluminescence and electroluminescence spectroscopy

All-inorganic cesium-lead-halide CsPbX3 (X = Cl, Br, and I) perovskite nanocrystals (NCs) have attracted great attention due to their outstanding photoelectric properties in recent years. However, the unsatisfactory optical stability and undesirable anion-exchange reaction between different halides of perovskite NCs seriously hinder their further development and application in optoelectronic devices. Herein, the intermediate stages during anion-exchange processes between as-prepared perovskite NCs after mixing into solution and film were respectively studied and characterized by using photoluminescence and electroluminescence (EL) spectroscopy. In our case, the physical collision and solvent bridge effect together affect the anion-exchange reaction of the mixed solution, while the physical collision mechanism is dominant in the mixed film. More importantly, a thin polystyrene layer was inserted between CsPbBr3 and CsPbI3 to efficiently prevent the halogen anion-exchange reaction. Color-tunable EL performance and stable white emission were successfully achieved by employing the optimized CsPbI3/PS/CsPbBr3 structures onto the blue-violet heterojunctions.

Uranyl complexes of p-t-butylcalix[8]arene as H-bond acceptors—subtle effects of the donors

Leaving a mixture of excess N,N,N′,N′-tetramethyl-1,4-butanediamine (Me4BDA) with p-t-butylcalix[8]arene (L) and [(UO2)(dmso)5](ClO4)2 in a 1:2 ratio in acetonitrile solution to stand for an extended period resulted in the deposition of a mixture of three different crystalline materials. Single crystal X-ray structural studies were carried out to determine that the three materials were the solvated uncomplexed macrocycle L.1.5MeCN, and two uranyl complexes. These were formulated as (Me4BDAH2)2+[(HO)(UO2)2(L-5H)]2–·9MeCN·H2O and (Me4BDAH2)2+[HO(UO2)2{L-5H)]2–·(Me3BDAH)+[H2O(UO2)2(L-5H)]−·Me4BDA·14MeCN·H2O·CH3OH respectively. In contrast to analogous systems based on 1,2-ethanediamine and 1,3-propanediamine derivatives, extension of the chain length separating the N-centres to (CH2)4 in the present systems has resulted in the formation of polymeric chains where the calixuranate anions are linked by H-bond acceptance from diammonium units. These links are still not completely direct and pass in part through solvent bridges. Direct double interactions do occur in the inverse situation where the calixarene acts as an H-bond donor to neutral 1,4-butanediamine species but lead only to dimerisation.

Insight into the drug resistance mechanisms of GS-9669 caused by mutations of HCV NS5B polymerase via molecular simulation

GS-9669 is a non-nucleos(t)ide inhibitor (NNI) binding to the thumb site II of the Hepatitis C virus (HCV) NS5B polymerase and has advanced into phase II trials. To clarify the drug resistance mechanisms of GS-9669 caused by M423T/I/V, L419M, R422K, and I482L mutations of NS5B polymerase (GT1b) and the receptor-ligand interactions during the binding process, a series of molecular simulation methods including molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed for the wild-type (WT) and six mutant NS5B/GS-9669 complexes. The calculated results indicate that the binding free energies of the mutant systems are less negative than that of the WT system, indicating that these mutations will indeed cause NS5B to produce different degrees of resistance to GS-9669. The mutation-induced drug resistances are mainly caused by the loss of binding affinities of Leu419 and Trp528 with GS-9669 or the formation of multiple solvent bridges. Moreover, the ASMD calculations show that GS-9669 binds to the thumb II sites of the seven NS5B polymerases in distinct pathways without any obvious energy barriers. Although the recognition methods and binding pathways are distinct, the binding processes of GS-9669 with the WT and mutant NS5B polymerases are basically controlled thermodynamically. This study clearly reveals the resistance mechanisms of GS-9669 caused by M423T/I/V, L419M, R422K, and I482L mutations of HCV NS5B polymerase and provides some valuable clues for further optimization and design of novel NS5B inhibitors.

Bridging solvent molecules mediate RNase A - Ligand binding.

Due to its high catalytic activity and readily available supply, ribonuclease A (RNase A) has become a pivotal enzyme in the history of protein science. Moreover, this great interest has carried over to computational chemistry and molecular dynamics, where RNase A has become a model system for various types of studies, all the while being an important drug design target in its own right. Here, we present a detailed molecular dynamics study of RNase-ligand binding involving 22 compounds, spanning nearly five orders of magnitude in affinity, and totaling 8.8 μs of sampling with the standard Amber parameters and an additional 8.8 μs of sampling with a modified potential. We show that short-lived, solvent-mediated bridging interactions are crucial to RNase-ligand binding. We characterize the behavior of bridging solvent molecules, uncovering a power-law dependence between the lifetime of a solvent bridge and the probability of its occurrence. We also demonstrate that from an energetic perspective, bridging solvent in RNase A-ligand binding behaves like part of the enzyme, rather than the ligands. Moreover, we describe an automated pipeline for the detection and processing of bridging interactions, and offer an independent assessment of the performance of the state-of-the-art fixed-charge force fields. Thus, our work has broad implications for drug design and computational chemistry in general.

Ultrafast Proton Transport between a Hydroxy Acid and a Nitrogen Base along Solvent Bridges Governed by the Hydroxide/Methoxide Transfer Mechanism.

Aqueous proton transport plays a key role in acid–base neutralization and energy transport through biological membranes and hydrogen fuel cells. Extensive experimental and theoretical studies have resulted in a highly detailed elucidation of one of the underlying microscopic mechanisms for aqueous excess proton transport, known as the von Grotthuss mechanism, involving different hydrated proton configurations with associated high fluxional structural dynamics. Hydroxide transport, with approximately 2-fold-lower bulk diffusion rates compared to those of excess protons, has received much less attention. We present femtosecond UV/IR pump–probe experiments and ab initio molecular dynamics simulations of different proton transport pathways of bifunctional photoacid 7-hydroxyquinoline (7HQ) in water/methanol mixtures. For 7HQ solvent-dependent photoacidity, free-energy–reactivity correlation behavior and quantum mechanics/molecular mechanics (QM/MM) trajectories point to a dominant OH–/CH3O– transport pathway for all water/methanol mixing ratios investigated. Our joint ultrafast infrared spectroscopic and ab initio molecular dynamics study provides conclusive evidence for the hydrolysis/methanolysis acid–base neutralization pathway, as formulated by Manfred Eigen half a century ago. Our findings on the distinctly different acid–base reactivities for aromatic hydroxyl and aromatic nitrogen functionalities suggest the usefulness of further exploration of these free-energy–reactivity correlations as a function of solvent polarity. Ultimately the determination of solvent-dependent acidities will contribute to a better understanding of proton-transport mechanisms at weakly polar surfaces and near polar or ionic regions in transmembrane proton pump proteins or hydrogen fuel cell materials.

Formulation and In- Vitro Evaluation of Spherical Crystal Agglomerates of Ebastine by Quasi Emulsion Solvent Diffusion Method

Ebastine (EBS) is a poorly water-soluble antihistaminic drug; it belongs to the class II group according to the biopharmaceutical classification system (BCS). The aim of the present work was to enhance the solubility, dissolution rate and micromeritic properties of the drug, by formulating it as spherical crystal agglomerates by Quasi Emulsion Solvent Diffusion (QESD) method.
 Spherical crystal agglomerates (SCAs) were prepared in presence of three solvents dichloromethane (DCM), water and chloroform as a good solvent, poor solvent and bridging solvent respectively. Agglomeration of EBS involved the use of some hydrophilic polymers like polyethylene glycol 4000 (PEG 4000), polyvinyl pyrrolidine K30 (PVP K30), D-?-tocopheryl polyethylene glycol 1000 succinate (TPGS) and ?. cyclodextrin. The pure drug (EBS) and its agglomerates with and without polymers were characterized for their drug content, percentage yield, solubility, in vitro drug release study and micromeritic property as well as by optical microscope, Scanning Electron Microscopy (SEM), FTIR spectroscopic studies, Differential Scanning Calorimetry (DSC) and X-ray Diffraction (XRD). The results of this work showed that there was a marketed enhancement in the solubility with improvement in dissolution rate, physiochemical properties, decrease in crystallinity and alteration in the crystal habit of the drug especially in presence of polymers. The best results were obtained with formula prepared by the combination of PEG 4000 and B. cyclodextrin in the agglomeration process of (EBS).

Inter-Backbone Charge Transfer as Prerequisite for Long-Range Conductivity in Perylene Bisimide Hydrogels.

Hydrogelation, the self-assembly of molecules into soft, water-loaded networks, is one way to bridge the structural gap between single molecules and functional materials. The potential of hydrogels, such as those based on perylene bisimides, lies in their chemical, physical, optical, and electronic properties, which are governed by the supramolecular structure of the gel. However, the structural motifs and their precise role for long-range conductivity are yet to be explored. Here, we present a comprehensive structural picture of a perylene bisimide hydrogel, suggesting that its long-range conductivity is limited by charge transfer between electronic backbones. We reveal nanocrystalline ribbon-like structures as the electronic and structural backbone units between which charge transfer is mediated by polar solvent bridges. We exemplify this effect with sensing, where exposure to polar vapor enhances conductivity by 5 orders of magnitude, emphasizing the crucial role of the interplay between structural motif and surrounding medium for the rational design of devices based on nanocrystalline hydrogels.

Ground-State Long-Range Proton Transfer Controlled by Proton-Accepting Ability of Hydrogen-Bonded Chains: A Theoretical Study

The ground-state triple proton transfer (GSTPT) reactions in HCOOH complexing with H2O, CH3OH, C2H5OH and mixed water–alcohol molecules were studied by quantum mechanical methods in the gas phase and in heptane. The triple proton transfer in HCOOH–S1–S2 (S1, S2 = H2O, CH3OH, C2H5OH) systems all occurred in an asynchronous but concerted protolysis mechanism. The formation pattern of the hydrogen-bonded chain was important to reduce the barrier height of the proton transfer process. When the hydrogen-bonded chain consisted of two identical CH3OH or C2H5OH molecules in the HCOOH–S1–S2 complexes, the GSTPT barrier height of HCOOH–S1–S2 decreased by more than 2 kcal mol−1 compared to that of HCOOH–H2O–H2O both in the gas phase and in heptane, because CH3OH and C2H5OH had larger proton-accepting abilities than had H2O. When the two solvent molecules in the hydrogen-bonded chain in the HCOOH–S1–S2 complexes were different, the barrier height of the proton transfer process varied depending on the proton-accepting ability (basicity) of the hydrogen-bonded chain. The bigger the proton-accepting ability (basicity) of the hydrogen-bonded chain, the lower the barrier height of the proton transfer process. Mixed bridging solvent molecules could accumulate their proton-accepting abilities and thus speeded up proton transfer. The solvent effect evidently decreased the zero point energy-corrected barrier heights of HCOOH clusters and increased the asynchronicity of the proton transfer, while the proton transfer mechanisms did not change in heptane.

Spectroscopy and DFT Calculations of a Flavo-diiron Enzyme Implicate New Diiron Site Structures.

Flavo-diiron proteins (FDPs) are non-heme iron containing enzymes that are widespread in anaerobic bacteria, archaea, and protozoa, serving as the terminal components to dioxygen and nitric oxide reductive scavenging pathways in these organisms. FDPs contain a dinuclear iron active site similar to that in hemerythrin, ribonucleotide reductase, and methane monooxygenase, all of which can bind NO and O2. However, only FDP competently turns over NO to N2O. Here, EPR and Mössbauer spectroscopies allow electronic characterization of the diferric and diferrous species of FDP. The exchange-coupling constant J (Hex = JS1·S2) was found to increase from +20 cm-1 to +32 cm-1 upon reduction of the diferric to the diferrous species, indicative of (1) at least one hydroxo bridge between the iron ions for both states and (2) a change to the diiron core structure upon reduction. In comparison to characterized diiron proteins and synthetic complexes, the experimental values were consistent with a dihydroxo bridged diferric core, which loses one hydroxo bridge upon reduction. DFT calculations of these structures gave values of J and Mössbauer parameters in agreement with experiment. Although the crystal structure shows a hydrogen bond between the iron bound aspartate and the bridging solvent molecule, the DFT calculations of structures consistent with the crystal structure gave calculated values of J incompatible with the spectroscopic results. We conclude that the crystal structure of the diferric state does not represent the frozen solution structure and that a mono-μ-hydroxo diferrous species is the catalytically functional state that reacts with NO and O2. The new EPR spectroscopic probe of the diferric state indicated that the diferric structure of FDP prior to and immediately after turnover with NO are flavin mononucleotide (FMN) dependent, implicating an additional proton transfer role for FMN in turnover of NO.

Solvent‐solubility‐parameter‐dependent homogeneity and sol–gel transitions of concentrated polyacrylonitrile solutions

ABSTRACTIn this study, we systematically explored the dependence of the homogeneity and sol–gel transition temperatures of various polyacrylonitrile (PAN) solutions on the solvent solubility parameters. The Cole–Cole slope was used to characterize the solution homogeneity, and we found that the PAN/dimethyl sulfoxide (DMSO) solution, which had a smaller Hansen solubility parameter distance between the solvent and PAN, showed better solution homogeneity than the PAN/dimethylformamide and PAN/dimethylacetamide solutions. Additionally, we found that both heating and cooling were able to cause the gelation of the PAN solution, although their mechanisms were totally different. The gelation caused by heating was ascribed to the nitrile–nitrile coupling of PAN chains, whereas the gelation caused by cooling was due to the solvent bridge effect. In this case, DMSO, which had the highest polarity and the strongest interactions with nitrile groups, caused the highest gelation temperature of the PAN solution during cooling. The gelation temperature of the PAN solution exhibits dependence on its solvent polarity. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 45405.

Electric‐field‐enhanced collection of laser‐ablated materials onto a solvent bridge for electrospray ionization mass spectrometry

Ambient imaging mass spectrometry methods are critically dependent on the ability to efficiently collect all substances from a well-defined area of the sample. Improvements in this area are critical and enabling. Methods for the efficient collection of laser-ablated materials directly into a solvent, for immediate transport to an ion source, have been explored using the application of electric fields. Electric-field-enhanced collection of laser-ablated materials has been demonstrated. Demonstrated increases in collection efficiency are as large as two orders of magnitude, in particular for hydrated biological materials, such as living bacterial colonies. This was achieved by applying approximately 1 kV between the sample and the receiving solvent surface. Electric-field-enhanced collection of laser-ablated materials holds great promise for ambient sampling and imaging mass spectrometry with rapid and direct interfacing to ionization sources, such as electrospray.

2-[(Adamantan-1-yl)aminomethyl]-4-chlorophenol hemihydrate

In the title compound, C17H22ClNO·0.5H2O, the water mol­ecule O atom resides on a twofold rotation axis. In the organic mol­ecule, the phenol group forms an intra­molecular O—H⋯N hydrogen bond. In the crystal, pairs of organic mol­ecules are hydrogen bonded through bridging solvent water mol­ecules, forming chains along the b-axis direction.

9-Phenyl-4,5-diaza-9H-fluoren-9-ol monohydrate.

The title compound, C17H12N2O·H2O, was synthesized by the reaction of 4,5-diaza­fluoren-9-one with a Grignard reagent in ether (the reaction mixture being hydrolysed with saturated NH4Cl solution), and crystallizes with two organic mol­ecules and two water mol­ecules in the asymmetric unit. The 4,5-diaza­fluorene fragment is approximately planar, with r.m.s. deviations of 0.0448 and 0.0198 Å in the two mol­ecules. The dihedral angles between the 4,5-diaza­fluorene planes and the phenyl ring are 80.49 (6) and 76.57 (7)°. The crystal packing features O—H⋯N and O—H⋯O hydrogen bonds involving the bridging solvent water mol­ecules, which link the mol­ecules into a three-dimensional network.

Ejection of Solvated Ions from Electrosprayed Methanol/Water Nanodroplets Studied by Molecular Dynamics Simulations

The ejection of solvated small ions from nanometer-sized droplets plays a central role during electrospray ionization (ESI). Molecular dynamics (MD) simulations can provide insights into the nanodroplet behavior. Earlier MD studies have largely focused on aqueous systems, whereas most practical ESI applications involve the use of organic cosolvents. We conduct simulations on mixed water/methanol droplets that carry excess NH(4)(+) ions. Methanol is found to compromise the H-bonding network, resulting in greatly increased rates of ion ejection and solvent evaporation. Considerable differences in the water and methanol escape rates cause time-dependent changes in droplet composition. Segregation occurs at low methanol concentration, such that layered droplets with a methanol-enriched periphery are formed. This phenomenon will enhance the partitioning of analyte molecules, with possible implications for their ESI efficiencies. Solvated ions are ejected from the tip of surface protrusions. Solvent bridging prior to ion secession is more extensive for methanol/water droplets than for purely aqueous systems. The ejection of solvated NH(4)(+) is visualized as diffusion-mediated escape from a metastable basin. The process involves thermally activated crossing of a ~30 kJ mol(-1) free energy barrier, in close agreement with the predictions of the classical ion evaporation model.

Probing osmolyte participation in the unfolding transition state of a protein

Understanding the molecular mechanisms of osmolyte protection in protein stability has proved to be challenging. In particular, little is known about the role of osmolytes in the structure of the unfolding transition state of a protein, the main determinant of its dynamics. We have developed an experimental protocol to directly probe the transition state of a protein in a range of osmolyte environments. We use an atomic force microscope in force-clamp mode to apply mechanical forces to the protein I27 and obtain force-dependent rate constants of protein unfolding. We measure the distance to the unfolding transition state, Δx(u), along a 1D reaction coordinate imposed by mechanical force. We find that for the small osmolytes, ethylene glycol, propylene glycol, and glycerol, Δx(u) scales with the size of the molecule, whereas for larger osmolytes, sorbitol and sucrose, Δx(u) remains the same as that measured in water. These results are in agreement with steered molecular dynamics simulations that show that small osmolytes act as solvent bridges in the unfolding transition state structure, whereas only water molecules act as solvent bridges in large osmolyte environments. These results demonstrate that novel force protocols combined with solvent substitution can directly probe angstrom changes in unfolding transition state structure. This approach creates new opportunities to gain molecular level understanding of the action of osmolytes in biomolecular processes.

Dicopper(II) complexes showing DNA hydrolase activity and monomeric adduct formation with bis(4-nitrophenyl)phosphate

Ferromagnetic dicopper(II) complexes [Cu2(μ-O2CCH3)(μ-OH)(L)2(μ-L1)](PF6)2, where L=1,10-phenanthroline (phen), L1=H2O in 1 and L=dipyrido[3,2-d:2′,3′-f]quinoxaline (dpq), L1=CH3CN in 2, are prepared and structurally characterized. Crystals of 1 and 2 belong to the monoclinic space group of P21/n and P21/m, respectively. The copper(II) centers display distorted square-pyramidal geometry having a phenanthroline base and two oxygen atoms of the bridging hydroxo and acetate group in the basal plane. The fifth coordination site has weak axially bound bridging solvent molecule H2O in 1 and CH3CN in 2. The Cu···Cu distances are 3.034 and 3.046Å in 1 and 2, respectively. The complexes show efficient hydrolytic cleavage of supercoiled pUC19 DNA as evidenced from the mechanistic studies that include T4 DNA ligase experiments. The binuclear complexes form monomeric copper(II) adducts [Cu(L)2(BNPP)](PF6) (L=phen, 3; dpq, 4) with bis(4-nitrophenyl)phosphate (BNPP) as a model phosphodiester. The crystal structures of 3 and 4 reveal distorted trigonal bipyramidal geometry in which BNPP binds through the oxygen atom of the phosphate. The kinetic data of the DNA cleavage reactions of the binuclear complexes under pseudo- and true-Michaelis–Menten conditions indicate remarkable enhancement in the DNA hydrolysis rate in comparison to the control data.

Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI

The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of functions; none have been visualized bound to DNA. The structure of the GIY-YIG restriction endonuclease R.Eco29kI has been solved both alone and bound to its target site. The protein displays a domain-swapped homodimeric structure with several extended surface loops encircling the DNA. Only three side chains from each protein subunit contact DNA bases, two directly and one via a bridging solvent molecule. Both tyrosine residues within the GIY-YIG motif are positioned in the catalytic center near a putative nucleophilic water; the remainder of the active site resembles the HNH endonuclease family. The structure illustrates how the GIY-YIG scaffold has been adapted for the highly specific recognition of a DNA restriction site, in contrast to nonspecific DNA cleavage by GIY-YIG domains in homing endonucleases or structure-specific cleavage by DNA repair enzymes such as UvrC.