Extensive Hydrogen-bonding Interactions Research Articles

Synthesis, structure, spectroscopy, thermal analysis and electron spin resonance of classical paddle–wheel binuclear and unusual polynuclear copper(II) compounds with benzoate and salicylamide

Two copper(II)benzoate compounds formulated in a fashion type of [Cux[RCOO]yLz] which are compound 1 or [Cu(C6H5COO)2(C6H5(OH)CONH2)]2 and compound 2 or [Cu(C6H5COO)(H2O)2]n·n(C6H5COO)·nH2O, {where (C6H5COO) = benzoate or (C6H5(OH)CONH2) = salicylamide}, have been successfully synthesized and characterized. Single crystal X-ray diffraction results confirmed the triclinic unit cell with a space group of P1¯ of the classical paddle–wheel binuclear compound 1 and the monoclinic unit cell with a space group of C2/c of polynuclear compound 2. Novel binuclear 1 has salicylamide as ancillary ligand and consists of a distorted square pyramidal [CuO4 + O] chromophore. Polynuclear 2 consists of the monomeric [Cu(C6H5CO)(H2O)2]n+ moiety which is furthered tribridged by coordinated ligands, generated the octahedral [CuO4 + O2] core and the polymeric [Cu(C6H5CO)(H2O)2]n+ chain. Compound 2 is stabilized by water and benzoate counter parts via CH⋯O and CH⋯π weak hydrogen bondings. The Fourier-Transform infrared spectrometer as well as the solid state ultraviolet visible spectra confirmed their components, geometries and weak interactions. The thermogravimetry analysis of compounds 1 and 2 started with the releasing of water molecules and were followed by the decompositions of the organic ligands. The thermograms also indicated the strong and extensive hydrogen bond interactions. The final thermal decomposition products were copper oxide. The electron spin resonance (ESR) spectra measured at room temperature illustrating the signals of triplet. The broader field ESR spectra of 2 than 1 are also noticed.

High-Performance and Rapid-Response Electrical Heaters Based on Ultraflexible, Heat-Resistant, and Mechanically Strong Aramid Nanofiber/Ag Nanowire Nanocomposite Papers.

High-performance and rapid response electrical heaters with ultraflexibility, superior heat resistance, and mechanical properties are highly desirable for the development of wearable devices, artificial intelligence, and high-performance heating systems in areas such as aerospace and the military. Herein, a facile and efficient two-step vacuum-assisted filtration followed by hot-pressing approach is presented to fabricate versatile electrical heaters based on the high-performance aramid nanofibers (ANFs) and highly conductive Ag nanowires (AgNWs). The resultant ANF/AgNW nanocomposite papers present ultraflexibility, extremely low sheet resistance (minimum Rs of 0.12 Ω/sq), and outstanding heat resistance (thermal degradation temperature above 500 °C) and mechanical properties (tensile strength of 285.7 MPa, tensile modulus of 6.51 GPa with a AgNW area fraction of 0.4 g/m2), benefiting from the partial embedding of AgNWs into the ANF substrate and the extensive hydrogen-bonding interactions. Moreover, the ANF/AgNW nanocomposite paper-based electrical heaters exhibit satisfyingly high heating temperatures (up to ∼200 °C) with rapid response time (10-30 s) at low AgNW area fractions and supplied voltages (0.5-5 V) and possess sufficient heating reliability, stability, and repeatability during the long-term and repeated heating and cooling cycles. Fully functional applications of the ANF/AgNW nanocomposite paper-based electrical heaters are demonstrated, indicating their excellent potential for emerging electronic applications such as wearable devices, artificial intelligence, and high-performance heating systems.

Atomically Thin Polymer Layer Enhances Toughness of Graphene Oxide Monolayers

Summary During the last decade, two-dimensional (2D) materials have emerged as versatile building blocks for the next generation of engineered materials. However, the intrinsically brittle behavior of 2D materials has thus far delayed their adoption in applications such as sensors and structural materials. Herein, we demonstrate a strategy for toughening graphene oxide (GO) through synergistic interfacial interactions between GO monolayers and ultrathin layers of strongly interacting poly(vinyl alcohol) (PVA). By creating GO-PVA and PVA-GO-PVA nanolaminates, we demonstrate a 2-fold increase in GO toughness, which translates into dramatic increases in energy dissipation and piercing resistance. Atomistic simulations show that this remarkable behavior arises from a polymer chain crack-bridging mechanism, resulting from a synergistic combination of interdomain reinforcements across the GO monolayer and extensive GO-polymer interfacial hydrogen-bonding interactions. The reported findings highlight the potential for achieving engineered 2D materials with superior mechanical properties by incorporating deformation and failure-resistant mechanics arising from tailored chemical interactions between constituents.

Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL).

Fucosylation of the N-glycan core via the α1-6 linkage (core fucosylation) is detected in specific types of cancers and related diseases, and thereby serves for a relevant biomarker. The lectin from a mushroom Pholiota squarrosa (PhoSL) shows a clear specificity to core fucosylation, without recognizing those with other types of fucosylation, such as the H type via the α1-2 linkage or the Lewis type via the α1-3 or α1-4 linkage. Here we determined the crystal structure of the PhoSL trimer in complex with a disaccharide fucose(α1-6)N-acetylglucosamine (GlcNAc). In the three sugar-binding pockets of PhoSL, extensive hydrophobic and hydrogen-bonding contacts were formed with the fucose moiety. In contrast, the GlcNAc moiety showed only a few hydrophobic and hydrogen-bonding contacts. To elucidate the mechanism for the specificity, we performed molecular dynamics simulations on this disaccharide and a trisaccharide fucose(α1-6)[GlcNAc(β1-4)]GlcNAc in complex with PhoSL. It was observed that the GlcNAc corresponding to the outer one of the N-glycan core entered the sugar-binding pocket with the N-acetyl group placed stably at the bottom, forming extensive hydrophobic and hydrogen-bonding interactions. In addition, these glycans adopted unstressed favorable conformations when bound to PhoSL. In contrast, H- and Lewis-types of fucosylated trisaccharides adopting favorable conformations caused inevitable steric hindrance with the steep edge of the binding pocket, when docked with PhoSL. Therefore, the specificity to core fucosylation of PhoSL was achieved by a combination of these preferential and exclusive mechanisms.

Ionic Assembly, Anion–π, Magnetic, and Electronic Attributes of Ambient Stable Naphthalenediimide Radical Ions

Organic spin-based molecular materials are considered to be attractive for the generation of functional materials with emergent optoelectronic, magnetic, or magneto-conductive properties. However, the major limitations to the utilization of organic spin-based systems are their high reactivity, instability, and propensity for dimerization. Herein, we report the synthesis, characterization, and magnetic and electronic studies of three ambient stable radical ions (1 a.+ , 1 b.+ , and 1 c.+ ). The radical ions 1 b.+ and 1 c.+ with BPh4 - and BF4 - counter anions, respectively, were synthesized in excellent yields by means of anion metathesis of 1 a.+ with Br- as its counter anion. Notably, synthesis of 1 a.+ was achieved in an ecofriendly, solvent-free protocol. The radical ions were characterized by means of single-crystal X-ray diffraction studies, which revealed the discrete nature of the radical ions and extensive hydrogen-bonding interactions within the radical ions and with the counter anions. Thus, radical ions can be organized to form infinite supramolecular arrays using weak noncovalent interactions. In addition, the Br- , BF4 - , and BPh4 - anions formed diverse types of anion-π interactions with the naphthalene and imide rings of the radical ions. The radical ions were characterized by means of X-band electron paramagnetic resonance (EPR) spectroscopy in solution and in the solid state. Magnetic studies revealed their paramagnetic nature in the range of 10 to 300 K. The radical ions exhibited high resistivity approaching the gigaohm (GΩ) scale. In addition, the radical ions exhibited panchromism.

Crystal structure and Hirshfeld surface analysis and of 2-ammoniumylmeth-yl-1H-benzimidazol-3-ium chloride monohydrate.

The asymmetric unit of the title compound, C8H11N3 2+·2Cl-·H2O, contains three organic cations, six chloride anions and three water mol-ecules of crystallization, which are connected by extensive hydrogen-bonding inter-actions into a three-dimensional supra-molecular architecture. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (37.4%), Cl⋯H/H⋯Cl (35.5%), C⋯H/H⋯C (9.5%) and C⋯C (6.9%) inter-actions.

Synthesis, structure and in vitro cytostatic activity study of the novel organotin(IV) derivatives of p-aminobenzenesulfonic acid

Four new p-aminobenzenesulfonate organotin complexes, [(n-Bu3Sn)(O3SC6H3-NH2-4)]n (1), [(n-Bu2Sn)4(O)2(OH)2(O3SC6H4-NH2-4)2] (2), [(Me2Sn)4(O)2(OH)2(O3SC6H4-NH2-4)2] (3) and [{(n-BuSn)12O14(OH)6}(O3SC6H4-NH2-4)2·3C4H8O2] (4·diox), were synthesized by reaction of p-aminobenzenesulfonic acid with tributyltin oxide, dibutyltin oxide, dimethyltin oxide and monobutyltin oxide, respectively. These complexes were characterized by elemental analysis, FT-IR, NMR (1H, 13C, 119Sn) spectroscopy as well as single-crystal X-ray diffraction. The crystal structure of complex 1 reveals that it is a 1D zig-zag chain structure and further interlinked into a 2D network by intermolecular interaction (N-H⋯O). The structure analysis indicates that complexes 2 and 3 are the ladder-like structure including three alternate Sn2O2 rings, and further result in the formation of a 3D supramolecular architecture for 2 and a 2D supramolecular network for 3 by extensive hydrogen-bonding interactions (O-H⋯O, N-H⋯O). Complex 4 exhibits a dodecanuclear organooxotin cages, which are connected into a hydrogen-bonded 2D structure. Furthermore, complexes 1-4 were evaluated for their in vitro cytostatic activity against the human lung cancer cells (A549) and the human hepatocellular carcinoma cells (HepG-2). The preliminary screen shows that organotin derivatives with increasing number n-butyl group exhibitsignificantly higher cytostatic activity, and much higher than methyl group.

Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab.

Monoclonal antibodies targeting PD-1/PD-L1 signaling pathway have achieved unprecedented success in cancer treatment over the last few years. Atezolizumab is the first PD-L1 monoclonal antibody approved by US FDA for cancer therapy; however the molecular basis of atezolizumab in blocking PD-1/PD-L1 interaction is not fully understood. Here we have solved the crystal structure of PD-L1/atezolizumab complex at 2.9 angstrom resolution. The structure shows that atezolizumab binds the front beta-sheet of PD-L1 through three CDR loops from the heavy chain and one CDR loop from the light chain. The binding involves extensive hydrogen-bonding and hydrophobic interactions. Notably there are multiple aromatic residues from the CDR loops forming Pi-Pi stacking or cation-Pi interactions within the center of the binding interface and the buried surface area is more than 2000 Å2, which is the largest amongst all the known PD-L1/antibody structures. Mutagenesis study revealed that two hot-spot residues (E58, R113) of PD-L1 contribute significantly to the binding of atezolizumab. The structure also shows that atezolizumab binds PD-L1 with a distinct heavy and light chain orientation and it blocks PD-1/PD-L1 interaction through competing with PD-1 for the same PD-L1 surface area. Taken together, the complex structure of PD-L1/atezolizumab solved here revealed the molecular mechanism of atezolizumab in immunotherapy and provides basis for future monoclonal antibody optimization and rational design of small chemical compounds targeting PD-L1 surface.

Adsorption, Assembly, and Oligomerization of Aspartic Acid on Pd(111)

The surface chemistry of l-aspartic acid is studied on Pd(111) in ultrahigh vacuum using reflection absorption infrared spectroscopy (RAIRS) and scanning tunneling microscopy (STM) as a function of sample temperature and coverage. Density functional theory (DFT) calculations are carried out to supplement the experimental results. At low temperatures, the dominant surface species was found to be monoaspartate species at all the experimental coverages. The monoaspartate species undergo extensive intermolecular hydrogen-bonding interactions and form extended two-dimensional ordered structures, forming either a honeycomb pattern or linear-row structures. At room temperature, aspartic acid undergoes a self-polymerization reaction to form oligosuccinimide networks, although some individual monoaspartate species are also observed.

Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator

Multiple antibiotic resistance regulator (MarR) family proteins are widely conserved transcription factors that control bacterial resistance to antibiotics, environmental stresses, as well as the regulation of virulence determinants. Escherichia coli MarR, the prototype member of this family, has recently been shown to undergo copper(II)-catalyzed inter-dimer disulfide bond formation via a unique cysteine residue (Cys80) residing in its DNA-binding domain. However, despite extensive structural characterization of the MarR family proteins, the structural mechanism for DNA binding of this copper(II)-sensing MarR factor remains elusive. Here, we report the crystal structures of DNA-bound forms of MarR, which revealed a unique, concerted generation of two new helix-loop-helix motifs that facilitated MarR's DNA binding. Structural analysis and electrophoretic mobility shift assays (EMSA) show that the flexibility of Gly116 in the center of helix α5 and the extensive hydrogen-bonding interactions at the N-terminus of helix α1 together assist the reorientation of the wHTH domains and stabilize MarR's DNA-bound conformation.

Conformational Dynamics and Protein–Substrate Interaction of ABC Transporter BtuCD at the Occluded State Revealed by Molecular Dynamics Simulations

ATP-binding cassette (ABC) transporters are ubiquitous in all three kingdoms of life and are implicated in many clinically relevant physiological processes. They couple the energy released by ATP hydrolysis to facilitate substrate translocation across cell membranes. The crystal structures of type II ABC importers have revealed their unique transmembrane domain architecture consisting of 10 transmembrane helices and their structurally conserved nucleotide-binding domains among all ABC transporters. However, molecular details of the interactions between the importers and their substrate remain largely elusive. Taking vitamin B12 importer BtuCD as an exemplar of type II importers, we investigated the dynamics of its occluded state and the detailed protein-substrate interactions using molecular dynamics simulation. Our trajectories show that the importer accommodates the substrate through a nonspecific binding mode as the substrate undergoes evident vertical and tilt motions inside the translocation cavity. Extensive hydrogen bond and hydrophobic interactions were observed between the substrate and the importer; however, most of these interactions are weak, with <38% occurrence. The presence of substrate leads to enlargement of the translocation cavity, especially at its cytoplasmic end, which may activate cytoplasmic regions and probably facilitate the transportation. The perturbations caused by periplasmic binding protein and nucleotides were also investigated. The study provides deeper insight into the translocation mechanism of BtuCD.

Energetic Salts Based on 3,5-Bis(dinitromethyl)-1,2,4-triazole Monoanion and Dianion: Controllable Preparation, Characterization, and High Performance.

Molecular modification of known explosives is considered to be an efficient route to design new energetic materials. A new family of energetic salts based on the 3,5-bis(dinitromethyl)-1,2,4-triazole monoanion and dianion were controllably synthesized by using 1-diamino-2,2-dinitroethene as a precursor. X-ray structure determination of monohydrazinium 3,5-bis(dinitromethyl)-1,2,4-triazolate (5) and monoammonium (6) and diammonium 3,5-bis(dinitromethyl)-1,2,4-triazolate hydrate (8·H2O) further confirmed the structures of these anions. In addition, as supported by X-ray data, in the monoanion system, the roving proton on the ring nitrogen rather than on the gem-dinitro carbon results in extensive hydrogen-bonding interactions and higher packing coefficients. Interestingly, 5 and 6 possess the highest calculated crystal densities, 1.965 and 1.957 g cm(-3) at 150 K, for hydrazinium and ammonium energetic salts, respectively. Energetic evaluation indicates that 5 (detonation velocity vD = 9086 m s(-1); detonation pressure P = 38.7 GPa) and 6 (vD, 9271 m s(-1); P = 41.0 GPa) exhibit great detonation properties, superior to those of current highly explosive benchmarks, such as 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX).

Local and Extended Structures of d-(−)-Tartaric Acid on Pd(111)

The structures of d-(−)-tartaric acid on the Pd(111) surface are studied by scanning tunneling microscopy (STM) supplemented by density functional theory (DFT) calculations as a function of coverage and sample temperature. When low coverages of d-(−)-tartaric acid were dosed with the sample at 300 K, and then cooled to 120 K for imaging, doubly dehydrogenated tartrate species (C2H4O62–) are observed, while at higher coverages, singly deprotonated bitartrate species (C2H5O61–) are prevalent. STM images show that the tartrate species are isolated on the surface, while the bitartrate species oligomerize by extensive hydrogen-bonding interactions. DFT calculations show that the adsorption of tartrate species locally disrupts the Pd lattice thereby imparting strain to the surface. The interaction between the two tartrate species in a dimeric pair is suggested to be the contribution of three factors: the adsorption-induced stress to the surface, Coulombic repulsion between the tartrate species, and the intermol...

Relative Binding Free Energies of Adenine and Guanine to Damaged and Undamaged DNA in Human DNA Polymeraseη: Clues for Fidelity and Overall Efficiency.

Human DNA polymerase η (Pol η) plays an essential protective role against skin cancer caused by cyclobutane thymine–thymine dimers (TTDs), a frequent form of DNA damage arising from exposure to the sun. This enzyme rescues stalled replication forks at the TTDs by inserting bases opposite these DNA defects. Herein we calculate binding free energies for a free deoxyribose nucleotide triphosphate, dATP or dGTP, to Pol η complexed with undamaged or damaged DNA. The calculations indicate that the binding of dATP to the enzyme–DNA complex is thermodynamically favored for TTD-containing DNA over undamaged DNA, most likely because of more extensive hydrogen-bonding interactions between the TTD and the enzyme that hold the TTD more rigidly in place. The calculations also illustrate that dATP binding is thermodynamically favored over dGTP binding at both thymine positions of the TTD, most likely due to more persistent and stable hydrogen-bonding interactions between the TTD and dATP than between the TTD and dGTP. This free energy difference is slightly greater for binding at the 5′ thymine position than at the 3′ thymine position, presumably because of stabilization arising from the A:T base pair formed at the 3′ position of the TTD in the previous step of Pol η function. All of these trends in binding free energies are consistent with experimental measurements of binding strength, fidelity, processivity, and overall efficiency. The insights gained from this analysis have implications for drug design efforts aimed at modifying the binding properties of this enzyme for improving cancer chemotherapy treatments.

Crystal structure of poly[[di-μ2-aqua-aqua-sodium] 4-amino-3,5,6-tri-chloro-pyridine-2-carboxyl-ate trihydrate], the sodium salt of the herbicide picloram.

In the structure of the title complex, {[Na(H2O)3](C6H2Cl3N2O2)·3H2O} n , the sodium salt of the herbicide picloram, the cation adopts a polymeric chain structure, based on μ2-aqua-bridged NaO5 trigonal-bipyramidal complex units which have, in addition, a singly bonded water mol-ecule. Each of the bridges within the chain, which extends parallel to the a axis, is centrosymmetric, with Na⋯Na separations of 3.4807 (16) and 3.5109 (16) Å. In the crystal, there are three water mol-ecules of solvation and these, as well as the coordinating water mol-ecules and the amino group of the 4-amino-3,5,6-tri-chloro-picolinate anion, are involved in extensive inter-species hydrogen-bonding inter-actions with carboxyl and water O atoms, as well as the pyridine N atom. Among these associations is a centrosymmetric cyclic tetra-water R 4 (4)(8) motif, resulting in an overall three-dimensional structure.

Two New Borates Made of [B5O6(OH)4]− and [B5O10(OH)]6− Clusters, Accompanying a Novel In Situ Organic Reaction

Two new pentaborate clusters, [MPD][B5O6(OH)4] (1, MPD = 2-methyl-1,4,5,6-tetrahydropyrimidine-3-ium) and SrB5O8(OH) H2O (2), have been hydro(solvo)thermally synthesized and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, powder X-ray diffraction and single-crystal X-ray structural analysis, respectively. Crystal data for 1: monoclinic, P21/c, a = 9.3384(3) A, b = 17.3774(5) A, c = 9.1886(3) A, β = 93.172(3)°, Z = 4. Crystal data for 2: triclinic, P-1, a = 6.6406(6) A, b = 6.6784(8) A, c = 10.2162(15) A, α = 98.905(11)°, β = 92.237(9)°, γ = 119.446(11)°, Z = 2. In compound 1, all the terminal O atoms of [B5O6(OH)4]− clusters are hydroxyl groups, which hinder the further connection of the [B5O6(OH)4]− clusters, only forming 3-D supramolecular frameworks via extensive hydrogen-bonding interactions. In compound 2, the [B5O10(OH)]6− clusters link each other to form a 2-D layer, which are further extended to 3-D supramolecular frameworks via extensive hydrogen-bonding interactions. Interestingly, a novel in situ organic reaction between 1,3-diaminoprapane and CH3COO− group has been observed during the formation of compound 1.

Two New Borates Containing [B5O6(OH)4] Clusters, Accompanying a Novel In Situ Organic Reaction Between Ethylenediamine and CH3COO− Group

Two new borate clusters, [C4H11N2O][C4H9N2][B5O6(OH)4]2 (1), [Cd(dien)2][B5O6(OH)4]2 (2, dien = diethylenetriamine), have been obtained under solvothermal conditions and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, powder X-ray diffraction and single-crystal X-ray structural analysis, respectively. Crystal data for 1: monoclinic, P21/c, a = 18.6975(5) A, b = 15.3413(8) A, c = 9.6691(3) A, β = 90.462(3)°, Z = 4. Crystal data for 2: triclinic, P-1, a = 8.6107(4) A, b = 9.3504(4) A, c = 18.9631(4) A, α = 103.798(4), β = 91.940(4)°, γ = 94.134(4)°, Z = 2. They all consist of [B5O6(OH)4]− clusters and further extend to 3-D frameworks via extensive hydrogen-bonding interactions. Interestingly, a novel in situ organic reaction between ethylenediamine and CH3COO− group has been observed during the formation of compound 1.

Post-translational modifications of histones that influence nucleosome dynamics.

Nucleosomes are efficient DNA-packaging units. The fundamental protein unit of the nucleosome is the histone dimer, a simple α-helical domain possessing a highly basic, curved surface that closely matches the phosphate backbone of bent duplex DNA. Two copies each of histone heterodimer, H3/H4 and H2A/H2B, form a histone octamer that is wrapped with approximately 146 bp of duplex DNA in a left-handed spiral1,2 (Figure ​(Figure1).1). Through extensive electrostatic and hydrogen-bonding interactions, each histone dimer coordinates three consecutive minor grooves on the inner surface of the DNA spiral. The bending of DNA over the protein surface brings the phosphate backbone of the two strands closer together on the inside of the spiral, narrowing the major and minor grooves of DNA, while widening the grooves on the outside. This bent conformation of the DNA duplex, which would otherwise be energetically unfavorable, is maintained through charge neutralization from numerous arginine and lysine side chains of the histones. Open in a separate window Figure 1 Overview of nucleosome architecture. (A) Illustration of H2A/H2B and H3/H4 heterodimers and how they fit together to form the histone octamer. (B) Face and top view of the nucleosome structure. For this and all subsequent molecular representations of the nucleosome, the high-resolution crystal structure (PDB code 1KX5) was used.93

Thermally stable 3,6-dinitropyrazolo[4,3-c]pyrazole-based energetic materials.

3,6-Dinitropyrazolo[4,3-c]pyrazole was prepared using an efficient modified process. With selected cations, ten nitrogen-rich energetic salts and three metal salts were synthesized in high yield based on the 3,6-dinitropyrazolo[4,3-c]pyrazolate anion. These compounds were fully characterized by IR and multinuclear NMR spectroscopies, as well as elemental analyses. The structures of the neutral compounds 4 and its salt 16 were confirmed by single-crystal X-ray diffraction showing extensive hydrogen-bonding interactions. The neutral pyrazole precursor and its salts are remarkably thermally stable. Based on the calculated heats of formation and measured densities, detonation pressures (22.5-35.4 GPa) and velocities (7948-9005 m s(-1)) were determined, and they compare favorably with those of TNT and RDX. Their impact and friction sensitivities range from 12 to >40 J and 80 to 360 N, respectively. These properties make them competitive as insensitive and thermally stable high-energy density materials.

Enzymatic hydrolysis of the β–β amide linkage in poly-β-aspartate

Polyaspartate is a biodegradable and water-soluble polymer, and an important material as an alternative to polyacrylate. Polyacrylate is widely used as a builder of detergents, pigment dispersant, cosmetic moisturizer, water treatment agents (scale preventive, metal corrosion preventive), water absorptive polymer of disposable diaper, and so on, and are likely accumulated in the environment. Replacement of the polymer by biodegradable polyaspartate should reduce the accumulation and therefore environmental pollution. Thermally synthesized polyaspartate contains both α- and β-amide linkages. Recently, three bacterial enzymes that degrade polyaspartate have been isolated and characterized. An enzyme from Pedobacter sp. KP-2 specifically catalyzes the hydrolysis of the β–β-amide linkage in the polymer. The enzyme is a monomeric periplasmic protein, and the mature form contains 265 amino acid residues with a molecular weight of about 30,000. To understand the mechanisms underlying the interactions with the polymer substrate and hydrolysis of the β–β amide linkage, we set out the crystallographic study of the enzyme. We succeeded in crystallization of the enzyme by vapor-diffusion using polyethylene glycol 4,000. Crystals belonged to orthorhombic space group C222. Addition of cobalt salt in the mother liquor altered the space group of crystals to P6422 and greatly improved the diffraction quality. Data sets for native and mutant enzymes were collected to a resolution of 1.9 Å at SPring-8, Japan. Phases were calculated by cobalt-SAD. The obtained structure represented an α/β hydrolase fold which is often observed for a large number of serine esterases such as lipase and PHB depolymerase. Residues Ser125, Asp193, and His248 were within hydrogen bonding interactions, forming a catalytic triad. Structures of subsites 1 and 2 for binding of monomer units of the polymer were determined for the mutant enzyme complexed with an oligomer substrate. The monomer unit bound to subsite 1 was in extensive hydrogen bond interactions with residues including arginine. Though overall structural similar between the enzyme and PHB depolymerase from Penicillium funiculosum, residues that may interact with polymer substrates were totally different.