Experimental Crystallographic Data Research Articles

The rotamer of the second-sphere histidine in AA9 lytic polysaccharide monooxygenase is pH dependent

Lytic polysaccharide monooxygenases (LPMOs) catalyze a reaction that is crucial for the biological decomposition of various biopolymers and for the industrial conversion of plant biomass. Despite the importance of LPMOs, the exact molecular-level nature of the reaction mechanism is still debated today. Here, we investigated the pH-dependent conformation of a second-sphere histidine (His) that we call the stacking histidine, which is conserved in fungal AA9 LPMOs and is speculated to assist catalysis in several of the LPMO reaction pathways.Using constant-pH and accelerated molecular dynamics simulations, we monitored the dynamics of the stacking His in different protonation states for both the resting Cu(II) and active Cu(I) forms of two fungal LPMOs. Consistent with experimental crystallographic and neutron diffraction data, our calculations suggest that the side chain of the protonated and positively charged form is rotated out of the active site toward the solvent. Importantly, only one of the possible neutral states of histidine (HIE state) is observed in the stacking orientation at neutral pH or when bound to cellulose. Our data predict that, in solution, the stacking His may act as a stabilizer (via hydrogen bonding) of the Cu(II)-superoxo complex after the LPMO-Cu(I) has reacted with O2 in solution, which, in fine, leads to H2O2 formation. Also, our data indicate that the HIE-stacking His is a poor acid/base catalyst when bound to the substrate and, in agreement with the literature, may play an important stabilizing role (via hydrogen bonding) during the peroxygenase catalysis.Our study reveals the pH titration midpoint values of the pH-dependent orientation of the stacking His should be considered when modeling and interpreting LPMO reactions, whether it be for classical LPMO kinetics or in industry-oriented enzymatic cocktails, and for understanding LPMO behavior in slightly acidic natural processes such as fungal wood decay.

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences.

We performed exhaustive torsion sampling on more than 3 million compounds using the GFN2-xTB method and performed a comparison of experimental crystallographic and gas-phase conformers. Many conformer sampling methods derive torsional angle distributions from experimental crystallographic data, limiting the torsion preferences to molecules that must be stable, synthetically accessible, and able to be crystallized. In this work, we evaluate the differences in torsional preferences of experimental crystallographic geometries and gas-phase computed conformers from a broad selection of compounds to determine whether torsional angle distributions obtained from semiempirical methods are suitable priors for conformer sampling. We find that differences in torsion preferences can be mostly attributed to a lack of available experimental crystallographic data with small deviations derived from gas-phase geometry differences. GFN2 demonstrates the ability to provide accurate and reliable torsional preferences that can provide a basis for new methods free from the limitations of experimental data collection. We provide Gaussian-based fits and sampling distributions suitable for torsion sampling and propose an alternative to the widely used "experimental torsion and knowledge distance geometry" (ETKDG) method using quantum torsion-derived distance geometry (QTDG) methods.

Theoretical study of the interaction between the antibiotic linezolid and the active site of the 50S ribosomal subunit of the bacterium Haloarcula marismortui.

First antibiotic in the oxazolidinone class, linezolid fights gram-positive multiresistant bacteria by inhibiting protein synthesis through its interaction with the 50S subunit of the functional bacterial ribosome. For its antimicrobial action, it is necessary that its chiral carbon located in the oxazolidinone ring is in the S-conformation. Computational calculation at time-dependent density functional theory methodology, ultraviolet-visible (UV-Vis), and electronic circular dichroism spectra was obtained for noncomplexed and complexed forms of linezolid to verify the possible chirality of nitrogen atom in the acetamide group of the molecule. The molecular system has two chiral centers. So, there are now four possible configurations: RR, RS, SR, and SS. For a better understanding of the system, the electronic spectra at the PBE0/6-311++G(3df,2p) level of theory were obtained. The complexed form was obtained from the crystallographic data of the ribosome, containing the S-linezolid molecular system. The computational results obtained for the electronic properties are in good agreement with the experimental crystallographic data and available theoretical results.

Structural and functional insights into the activation of the dual incision activity of UvrC, a key player in bacterial NER.

Bacterial nucleotide excision repair (NER), mediated by the UvrA, UvrB and UvrC proteins is a multistep, ATP-dependent process, that is responsible for the removal of a very wide range of chemically and structurally diverse DNA lesions. DNA damage removal is performed by UvrC, an enzyme possessing a dual endonuclease activity, capable of incising the DNA on either side of the damaged site to release a short single-stranded DNA fragment containing the lesion. Using biochemical and biophysical approaches, we have probed the oligomeric state, UvrB- and DNA-binding abilities and incision activities of wild-type and mutant constructs of UvrC from the radiation resistant bacterium, Deinococcus radiodurans. Moreover, by combining the power of new structure prediction algorithms and experimental crystallographic data, we have assembled the first model of a complete UvrC, revealing several unexpected structural motifs and in particular, a central inactive RNase H domain acting as a platform for the surrounding domains. In this configuration, UvrC is maintained in a 'closed' inactive state that needs to undergo a major rearrangement to adopt an 'open' active state capable of performing the dual incision reaction. Taken together, this study provides important insight into the mechanism of recruitment and activation of UvrC during NER.

How do density functionals affect the Hirshfeld atom refinement?

In this work, the effect of mixing different amounts of Hartree-Fock (HF) exchange with hybrid density functionals applied to the Hirshfeld atom refinement (HAR) of urea and oxalic acid dihydrate is explored. Together, the influence of using different basis sets, methods (including MP2 and HF) and cluster sizes (to model bulk effects) is studied. The results show that changing the amount of HF exchange, no matter the level of theory, has an impact almost exclusively on the H atom refinement parameters. Contrary to pure quantum mechanical calculations where good geometries are obtained with intermediate HF exchange mixtures, in the HAR the best match with neutron diffraction reference values is not necessarily found for these admixtures. While the non-hydrogen covalent bond lengths are insensitive to the combination of method or basis set employed, the X-H bond lengths always increase proportionally to the HF exchange for the analysed systems. This outcome is opposite to what is normally observed from geometry optimisations, i.e., shorter bonds are obtained with greater HF exchange. Additionally, the thermal ellipsoids tend to shrink with larger HF exchange, especially for the H atoms involved in strong hydrogen bonding. Thus, it may be the case that the development of density functionals or basis sets suitable for quantum crystallography should take a different path than those fitted for quantum chemistry calculations.

Low-Power Laser Ignition of an Antenna-Type Secondary Energetic Copper Complex: Synthesis, Characterization, Evaluation, and Ignition Mechanism Studies.

In recent years, development of new energetic compounds and formulations, suitable for ignition with relatively low-power lasers, is a highly active and competitive field of research. The main goal of these efforts is focused on achieving and providing much safer solutions for various detonator and initiator systems. In this work, we prepared, characterized, and studied thermal and ignition properties of a new laser-ignitable compound, based on the 5,6-bis(ethylnitroamino)-N'2,N'3-dihydroxypyrazine-2,3-bis(carboximidamide) (DS3) proligand. This new energetic proligand was prepared in three steps, starting with 5,6-bis(ethylamino)-pyrazine-2,3-dicarbonitrile. Crystallography studies of the DS3-derived Cu(II) complex (DS4) revealed a unique stacked antenna-type structure of the latter compound. DS4 has an exothermal temperature of 154.5 °C and was calculated to exhibit a velocity of detonation of 6.36 km·s-1 and a detonation pressure of 15.21 GPa. DS4 showed properties of a secondary explosive, having sensitivity to impact, friction, and electrostatic discharge of 8 J, 360 N, and 12 mJ, respectively. In order to study the mechanism of ignition by a laser (using a diode laser, 915 nm), we conducted a set of experiments that enabled us to characterize a photothermal ignition mechanism. Furthermore, we found that a single pulse, with a time duration of 1 ms and with a total energy of 4.6 mJ, was sufficient for achieving a consistent and full ignition of DS4. Dual-pulse experiments, with variable time intervals between the laser pulses, showed that DS4 undergoes ignition via a photothermal mechanism. Finally, calculating the chemical mechanism of the formation of the complex DS4 and modeling its anhydrous and hydrated crystal structures (density functional theory calculations using Gaussian and HASEM software) allowed us to pinpoint a more precise location of water molecules in experimental crystallographic data. These results suggest that DS4 has potential for further development to a higher technology readiness level and for integration into small-size safe detonator systems as for many civil, aerospace, and defense applications.

Density Function Theory calculation, and phthalonitrile process for a synthesis of single crystal zinc phthalocyanine

This study aims to synthesize the β-phase single crystal of zinc phthalocyanine (ZnPc) by using phthalonitrile process and vapor deposition. The single-crystal X-ray diffraction was used to identify the molecular structure and lattice parameters of the synthesized material. The molecular structure, frontier molecular orbitals, and IR spectroscopy of ZnPc were investigated through Time Dependent (TD)-Density Function Theory (DFT) calculations that is compared with experimental results. For the solid-state simulation, the experimental crystallographic data was used to determine band structure and density of state using DFT method on Quantum Espresso. The β-phase monoclinic single crystal of ZnPc is as a direct band gap semiconductor with the calculated energy gap of 2.1 eV, and the Fermi energy level of 2.61 eV.

Structural-Spectroscopic Properties and Antioxidant Activity Studies of Naringenin in Solvent Media

In this study, solvent effects on the structural and spectroscopic properties of the naringenin have been investigated. Geometric parameters were calculated and were compared with the experimental X-ray crystallographic data. In addition, optimized structures were obtained in solvent media and the solvents effects on geometric parameters were determined. Vibrational modes obtained in the vacuum and in solvent environments were compared with the experimental IR spectrum. Furthermore, the HOMO-LUMO energies and chemical reactivity were also determined. Antioxidant activity of naringenin has been investigated with hydrogen atom abstraction from −OH groups. The bond dissociation enthalpies have been calculated and it is determined that this process should be the main mechanism for the antioxidant activity of naringenin. According to the calculation results, surprisingly, it has been found that in DMSO, BDE values of naringenin are significantly reduced and thus antioxidant activity is increased compared to other media.

OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field.

The great importance of pH for molecular processes has motivated the continuous development of numerical methods to improve the physical description of molecular mechanisms in computer simulations. Although rigid titration models are able to provide several pieces of useful information, the coupling between the molecular conformational changes and the acid-base equilibrium is necessary to more completely model the pH effects in biomolecules. Previously reported convergence issues with atomistic simulations indicated that a promising approach would require coarse-grained models. By means of the coupling between the successful OPEP force field for proteins with the fast proton titration scheme, we proposed a new protocol for constant-pH molecular dynamics simulations that takes advantage of both coarse-grained approaches to circumvent sampling difficulties faced by other numerical schemes and also to be able to properly describe electrostatic and structural properties at lower CPU costs. Here, we introduce this new protocol that defines now OPEP6 and its p Ka's benchmark for a set of representative proteins (HP36, BBL, HEWL, NTL9, and a protein G variant). In comparison with experimental measurements, our calculated p Ka values have the average, maximum absolute, and root-mean-square deviations of [0.3-1.1], [0.6-2.5], and [0.4-1.3] pH units, respectively, for these five studied proteins. These numbers are within the ones commonly observed when similar comparisons are done among different theoretical models and are slightly better than the accuracy obtained by a rigid model using the same titration engine. For BBL, the predicted p Ka are closer to experimental results than other analyzed theoretical data. Structural properties were tested for insulin where separation distances between the groups were compared and found in agreement with experimental crystallographic data obtained at different pH conditions. These indicate the ability of the new OPEP to properly describe the system physics and open up more possibilities to study pH-mediated biological processes.

Effect of fluorosubstitution and central metals on the molecular structure and vibrational spectra of metal phthalocyanines

In this work, the effect of fluorosubstitution in metal phthalocyanines (MPc) on their molecular structure and vibrational spectra is studied. For this purpose, the IR- and Raman spectra of unsubstituted (FePc), tetrafluorosubstituted (FePcF4) and hexadecafluorosubstituted iron phthalocyanines as well as isotopic wavenumber shifts upon 15N substitution in FePc and FePcF4 were investigated experimentally and theoretically. The calculated geometries of molecules were compared with the experimental crystallographic data obtained by the single crystal structure refinement. The density functional theory (DFT) calculations were used for the analysis of IR- and Raman spectra of these three derivatives. Several groups of vibrations most sensitive to fluorosubstitution have been revealed. Apart from the influence of F-substitution, the effect of different central metal ions (M = Cu, Co, Zn, Fe, Pd, VO, Pb) on the structure and vibrational spectra of MPc, MPcF4 and MPcF16 is also discussed.

Conformational Space Analysis of Protected N-Formyl-L-Phenylalanine-N-Amide Amino Acid: Effects of the Intramolecular Basis Set Superposition Error

In the present work, the conformational space landscape of L-phenylalanine amino acid with protected N- and C-termini (HCO–L–Phe–NH2) is explored using an efficient genetic algorithm combined with DFT and MP2 calculations in order to investigate all potential minima on its potential energy surface (PES). The calculations carried out on this system reveal that conformational building units corresponding to the right-handed helix (αL [φPhe = −60°, ψPhe = −60°]) and polyproline II (eL [φPhe = −60°, ψPhe = 180°]) are still missing from its PES and the inverse gamma turn (γL [φPhe = −60°, ψPhe = 60°]) form is preferred for this compound in accordance with the ab initio and DFT calculation results. Furthermore, this study shows that the sensitivity of the conformational preference of HCO–L–Phe–NH2 structures from B3LYP to MP2 optimizations is due to a significant contribution of the basis set superposition error (BSSE) effect and the 6-311++G(2d,2p) basis set is more suitable for the estimation of intramolecular interactions within this residue. The comparison between the theoretical calculations and the experimental X-ray crystallographic data extracted from the protein data bank (PDB) shows promising similarities, which opens the way for possible future applications on large molecular systems.

Synthesis of α-(4-Oxazolyl)amino Esters via Brønsted Acid Catalyzed Tandem Reaction.

A one-step, Brønsted acid catalyzed tandem reaction for the synthesis of α-(4-oxazolyl)amino esters was developed. 4-Nitrobenzenesulfonic acid was found to be an efficient catalyst for the coupling of ethyl 2-oxobut-3-ynoates with amides to provide various α-(4-oxazolyl)amino esters. The experimental and X-ray crystallographic data suggest that a series of bond-forming reactions including imine formation, intermolecular Michael addition, and intramolecular Michael addition are involved to generate both the oxazole and amino acid functionalities.

Study of the In2O3 molecule in the free state and in the crystal

ABSTRACTThe nanomaterials based on the In2O3 molecule are widely used as catalysts and sensors among other applications. In the present study, we discuss the possibility of using nanoclusters of In2O3 as molecular photomotors. A comparative analysis of the electronic structure of the In2O3 molecule in the free state and in the crystal is performed. For the free In2O3 molecule the geometry of its lowest structures, V-shape and linear, was optimised at the CCSD(T) level, which is the most precise computational method applied up to date to study In2O3. Using experimental crystallographic data, we determined the geometry of In2O3 in the crystal. It has a zigzag, not symmetric structure and possesses a dipole moment with magnitude slightly smaller than that of the V-structure of the free molecule (the linear structure due to its symmetry has no dipole moment). According to the Natural Atomic population analysis, the chemical structure of the linear In2O3 can be represented as O = In−O−In = O; the V-shaped molecule has the similar double- and single-bond structure. The construction of nanoclusters from ʻbricksʼ of In2O3 with geometry extracted from crystal (or nanoclusters extracted directly from crystal) and their use as photo-driven molecular motors are discussed.

Evaluating Competing Intermolecular Interactions through Molecular Electrostatic Potentials and Hydrogen-Bond Propensities

The structural chemistry of six thiazole amides has been explored using experimental crystallographic data, and a combination of calculated hydrogen-bond propensities (HBPs) and hydrogen-bond energies. Both methods correctly identify the main hydrogen-bonded synthon, a pairwise N–H···N dimer, which appears in all the available structures. The strength and stability of the homosynthon in these compounds were tested by attempting to co-crystallize all six compounds with 20 different carboxylic acids. A total of 120 attempted reactions were carried out via liquid-assisted grinding experiments; sixty of these reactions produced a co-crystal, as indicated by IR spectroscopy. HBP calculations were employed in order to try to predict which of the 120 reactions would be successful. A multi-component score (MC score) was obtained from the hydrogen-bond propensity calculations, and this score coupled with a cut-off value >0.0 resulted in a 77% agreement between prediction and experiment (88% success for aliphatic a...

Exploring the electronic structure of Pb2+ ions containing material Pb16(OH)16(NO3)16

A theoretical band structure calculation for lead nitrate hydroxide Pb16(OH)16(NO3)16 single crystal was performed based on the experimental crystallographic data obtained by Chang et al. Calculations exhibit that the conduction band minimum (CBM) is situated at Γ the center of the Brillouin zone (BZ) while the valence band maximum (VBM) is located between Γ and Y points of the BZ, resulting in an indirect energy band gap of about 3.70eV in close agreement to the measured one (3.78eV). The angular momentum resolved projected density of states reveals the existence of the strong hybridization between the orbitals and the VBM is originated from Pb-6s/6p and O-2p orbitals while the CBM from N-2p and Pb-6p orbitals. The calculated valence electronic charge density distribution explore the bond characters and the dominancy of the covalent bonding between Pb–O of PbOn ployhedra and N–O of [NO3]− triangle. The calculated bond lengths and angles show good agreement with the experimental data.

Lead nitrate hydroxide: A strong second-order optical nonlinearity acentric crystal with high laser damage thresholds

A comprehensive theoretical calculation for the complex first-order linear and the second-order non-linear optical dispersion of acentric lead nitrate hydroxide (Pb16(OH)16(NO3)16) single crystals was performed based on the experimental crystallographic data obtained by Chang et al. [Inorg. Chem. 53, 3320–3325 (2014)]. Calculations show an energy band gap of about 3.70 eV, in close agreement to the measured one (3.78 eV). The energy gap value confirms that the Pb16(OH)16(NO3)16 single crystal exhibits an exceptional laser damage threshold. The complex first-order linear optical dispersion helps to get deep insight into the electronic structure and reveals the existence of considerable anisotropy, negative uniaxial anisotropy, and positive birefringence. The calculated second harmonic generation of Pb16(OH)16(NO3)16 at wavelength (λ = 1064 nm) shows a good agreement with the reported measured value. In addition, the microscopic first hyperpolarizability was obtained at the static limit and at the wavelength 1064 nm.

Competition between Polar and Centrosymmetric Packings in Molecular Crystals: Analysis of Actual and Virtual Structures

Imines obtained by condensation of 4-hydroxybenzohydrazide with aliphatic ketones are a rare example of a class of compounds showing a remarkable tendency to crystallize in acentric polar space groups (Pna21 or Cc). In fact, all of the (seven) compounds studied up to now show at least one polar polymorph. In some cases, polymorphism was detected, and a nonpolar centrosymmetric phase was also identified (P21/c or P21/n space group). With the aim to disclose the conditions that can favor the formation of acentric structures in molecular crystals, we report, in this paper, a theoretical analysis (ab initio density functional theory with periodic boundary) of the lattice energy and density of all the packing modes observed in the whole set of imines. The computational analysis has been performed by optimizing each compound in its own experimental packings (actual crystal structures) and also in the packings of the other compounds of the class (virtual structures). The experimental crystallographic data and the theoretical analysis suggest that two conformers, basically differing for the orientation of the phenolic H atom in the plane of the phenyl ring, compete, in solution, for the formation of polar or centrosymmetric packings. The transitions between polar and centrosymmetric polymorphs are of diffusive type, and single crystals are not preserved, while the transitions between different polar polymorphs can be of single-crystal-to-single-crystal type.

Zn···Zn interactions at nickel and palladium centers.

The analogy between ZnR fragments and the hydrogen radical represents a fruitful concept in organometallic synthesis. The organozinc(ii) and -zinc(i) sources ZnMe2 (Me = methyl) and [Zn2Cp*2] (Cp* = pentamethylcyclopentadienyl) provide one-electron fragments ·ZnR (R = Me, Cp*), which can be trapped by transition metal complexes [L a M], yielding [L b (ZnR) n ]. The addition of the dizinc compound [Zn2Cp*2] to coordinatively unsaturated [L a M] by the homolytic cleavage of the Zn-Zn bond can be compared to the classic oxidative addition reaction of H2, forming dihydride complexes [L a M(H)2]. It has also been widely shown that dihydrogen coordinates under preservation of the H-H bond in the case of certain electronic properties of the transition metal fragment. The σ-aromatic triangular clusters [Zn3Cp*3]+ and [Zn2CuCp*3] may be regarded as the first indication of this so far unknown, side-on coordination mode of [Zn2Cp*2]. With this background in mind the question arises if a series of complexes featuring the Zn2M structural motif can be prepared exhibiting a (more or less) intact Zn-Zn interaction, i.e. di-zinc complexes which are analogous to non-classical dihydrogen complexes of the Kubas type. In order to probe this idea, a series of interrelated organozinc nickel and palladium complexes and clusters were synthesized and characterized as model compounds: [Ni(ZnCp*)(ZnMe)(PMe3)3] (1), [Ni(ZnCp*)2(ZnMe)2(PMe3)2] (2), [{Ni(CN t Bu)2(μ2-ZnCp*)(μ2-ZnMe)}2] (3), [Pd(ZnCp*)4(CN t Bu)2] (4) and [Pd3Zn6(PCy3)2(Cp*)4] (5). The dependence of Zn···Zn interactions as a function of the ligand environments and the metal centers was studied. Experimental X-ray crystallographic structural data and DFT calculations support the analogy between dihydrogen and dizinc transition metal complexes.

PRIGo: a new multi-axis goniometer for macromolecular crystallography.

The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0-90°), followed by a ϕ stage (0-360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

Three-dimensional structures of laccases.

Laccases are phenol oxidases that belong to the family of multi-copper oxidases and the superfamily of cupredoxins. A number of potential industrial applications for laccases have led to intensive structure-function studies and an increased amount of crystal structures has been solved. The objective of this review is to summarize and analyze available crystal structures of laccases. The experimental crystallographic data are now easily available from the websites and electron density maps can be used for the interpretation of the structural models. The crystal structures can give valuable insights into the functional mechanisms and may serve as the basis for the development of laccases for industrial applications.