Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods

A computational chemistry analysis of six unique tautomers of cyromazine, a pesticide used for fly control, was performed with density functional theory (DFT) and canonical second-order Møller–Plesset perturbation theory (MP2) methods to gain insight into the contributions of molecular structure to detection properties. Full geometry optimisation using the 6-311++G** basis set provided energetic properties, natural charges, frontier orbitals and vibrational modes. Excitation energies were obtained using time-dependent DFT. Hydrogen location and bond order contribute significantly to the electronic properties. The common cyromazine tautomer possesses the lowest energy, highest band gap energy and highest excitation energy. B3LYP/6-31G** dynamics simulations indicate each tautomer possesses a stable structure with limited rotation about the single bonds. Tautomerisation involving intramolecular hydrogen transfer influences the natural charges of neighbouring atoms and the frontier orbital properties. The excitation energies are highly correlated with band gap energies of the frontier orbitals. The calculated infrared and Raman spectra are suitable for vibrational assignments associated with the chemical structure. The tautomeric forms of cyromazine possess similar spatial properties and significant variation in electronic properties.     

A role for hydrophobicity in a Diels–Alder reaction catalyzed by pyridyl-modified RNA

New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu²⁺, as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification''s role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism.     

π-π stacking tackled with density functional theory

Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing pi-pi stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound pi-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the pi-pi stacking potential energy surface.     

Density functional theory investigations of NiN2S2 reactivity as a function of nitrogen donor type and N–H···S hydrogen bonding inspired by nickel-containing superoxide dismutase

Density functional theory calculations on a series of six square-planar NiN₂S₂ complexes have been performed. The nitrogen donor type was varied from diamino in Ni(bme-dmed), 1, to amino-amido in [Ni(mama)]⁻, 2, to diamido in [Ni(ema)]²⁻, 3. The sulfur-oxygenated derivative Ni(bme-O₂-dmed), 4, and hydrogen-bonded derivatives (5 and 6) of 2 and 3 were also studied. Full geometric optimization and subsequent population analyses were performed using the 6–311g(d,p) basis set. The frontier molecular orbitals for all complexes contain significant nickel and sulfur character. Molecular electrostatic potentials show that amido nitrogen donors increase electron density at nickel relative to sulfur. Sulfur modification further shifts electron density away from the ligand towards the metal. It is proposed that the nitrogen donor type and sulfur modification may regulate sulfur-site reactivity in nickel-containing superoxide dismutase.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine–cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)_ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.     

Highly efficient method for 125I-radiolabeling of biomolecules using inverse-electron-demand Diels–Alder reaction

In this report, we present a rapid and highly efficient method for radioactive iodine labeling of trans-cyclooctene group conjugated biomolecules using inverse-electron-demand Diels–Alder reaction. Radioiodination reaction of the tetrazine structure was carried out using the stannylated precursor 2 to give ¹²⁵I-labeled product ([¹²⁵I]1) with high radiochemical yield (65 ± 8%) and radiochemical purity (>99%). For radiolabeling application of [¹²⁵I]1, trans-cyclooctene derived cRGD peptide and human serum albumin were prepared. These substrates were reacted with [¹²⁵I]1 under mild condition to provide the radiolabeled products [¹²⁵I]6 and [¹²⁵I]8, respectively, with excellent radiochemical yields. The biodistribution study of [¹²⁵I]8 in normal ICR mice showed significantly lower thyroid uptake values than that of ¹²⁵I-labeled human serum albumin prepared by a traditional radiolabeling method. Therefore [¹²⁵I]8 will be a useful radiolabeled tracer in various molecular imaging and biological studies. Those results clearly demonstrate that [¹²⁵I]1 will be used as a valuable prosthetic group for radiolabeling of biomolecules.     

Molecular structure,vibrational spectra and HOMO,LUMO analysis of 4-piperidone by density functional theory and ab initio Hartree–Fock calculations

Vibrational frequencies and geometrical parameters of 4-piperidone (4-PID) in the ground state have been calculated by using the Hartree–Fock (HF) and density functional methods (B3LYP) with 6-311++G(d,p) and 6-311+G(3df,2p) basis sets. These methods are proposed as a tool to be applied in the structural characterisation of 4-PID (C₅H₉NO). The title molecule has C _s point group symmetry, thus providing useful support in the interpretation of experimental IR and Raman data. The DFT-B3LYP/6-311+G(3df,2p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 4-PID. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital energies show that charge transfer occurs within the molecule. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

Transformation of the θ-phase in Mg-Li-Al alloys: a density functional theory study

In Mg-Li-Al alloys, θ-phase MgAlLi₂ is a strengthening and metastable phase which is liable to be transformed to the equilibrium phase AlLi on overaging. While the structural details of the θ-phase MgAlLi₂ and the microscopic transformation are still unknown. In this paper, the structure of MgAlLi₂ unit cell was determined through X-ray powder diffraction simulation. Microscopic transformation process of θ-phase MgAlLi₂ was discussed in detail using first principles method.     

Molecular structure and vibrational spectra of 4-nitrobenzylchloride by ab initio Hartree–Fock and density functional methods

The Fourier transform Raman and Fourier transform infrared spectra 4-nitrobenzylchloride of (NBC) were recorded in the solid phase. The Fourier transform gas phase infrared spectrum of NBC was also recorded. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF/DFT (B3LYP and BLYP) and SVWN methods with the 6-31G(d,p) basis set. The scaled theoretical wave numbers by B3LYP showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of NBC is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.     

Electronic structure simulations of 2,6-dimethyl-2,5-heptadien-4-one by FTIR,FT-Raman,NMR, UV–vis,NBO and density functional theory

Density functional theory (DFT) (B3LYP and B3PW91) calculations have been carried out for 2,6-dimethyl-2,5-heptadien-4-one (DMHD4O) using 6–311++ G** basis set. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out from the FTIR and FT-Raman spectral data. The theoretical electronic absorption has been calculated by using time-dependent DFT (TD-DFT) methods and compared with the experimental spectra. The theoretically computed Frontier energy gaps and TD-DFT calculations are in good agreement with the experimental UV–vis spectral absorption. The chemical hardness measured from the Frontier molecular orbital energies of DMHD4O is 0.0693 eV. Electronic stability of the compound arising from hyperconjugative interactions and charge delocalisation were also investigated based on the natural bond orbital (NBO) analysis. Effective stabilisation energy E ⁽²⁾ associated with the interactions of the π and the lone pair of electrons was determined by the NBO analysis. ¹³C and ¹H NMR chemical shifts of the compound have been calculated by means of Gauge-Invariant Atomic Orbital using B3LYP/6–311++ G** method. The partial ionic character of the carbonyl group due to resonance render a partially positive charge to the carbonyl carbon, and thus C4 chemical shift lie in the very downfield 191.6 ppm. Comparison between the experimental and the theoretical results indicates that B3LYP method is able to provide satisfactory results for predicting vibrational, electronic and NMR properties.     

Elasticity–density and viscoelasticity–density relationships at the tibia mid-diaphysis assessed from resonant ultrasound spectroscopy measurements

Cortical bone tissue is an anisotropic material characterized by typically five independent elastic coefficients (for transverse isotropy) governing shear and longitudinal deformations in the different anatomical directions. It is well established that the Young’s modulus in the direction of the bone axis of long bones has a strong relationship with mass density. It is not clear, however, whether relationships of similar strength exist for the other elastic coefficients, for they have seldom been investigated, and the results available in the literature are contradictory. The objectives of the present work were to document the anisotropic elastic properties of cortical bone at the tibia mid-diaphysis and to elucidate their relationships with mass density. Resonant ultrasound spectroscopy (RUS) was used to measure the transverse isotropic stiffness tensor of 55 specimens from 19 donors. Except for Poisson’s ratios and the non-diagonal stiffness coefficient, strong linear correlations between the different elastic coefficients \((0.7 < {r^{2}} < 0.99)\) and between these coefficients and density \((0.79 < {r^{2}} < 0.89)\) were found. Comparison with previously published data from femur specimens suggested that the strong correlations evidenced in this study may not only be valid for the mid-tibia. RUS also measures the viscous part of the stiffness tensor. An anisotropy ratio close to two was found for damping coefficients. Damping increased as the mass density decreased. The data suggest that a relatively accurate estimation of all the mid-tibia elastic coefficients can be derived from mass density. This is of particular interest (1) to design organ-scale bone models in which elastic coefficients are mapped according to Hounsfield values from computed tomography scans as a surrogate for mass density and (2) to model ultrasound propagation at the mid-tibia, which is an important site for the in vivo assessment of bone status with axial transmission techniques.     

Structure of Lennard–Jones fluid near large spherical particles: further test of the “universality” of adjustable parameter in perturbation density functional theory

Grand canonical Monte Carlo simulation is used to study the density profiles of Lennard–Jones (LJ) fluid next to a large hard sphere (mimicking a colloidal particle) of various sizes. The LJ fluid in the inhomogeneous system thus maintains equilibrium with the bulk LJ fluid. The chosen density and potential parameters for the bulk fluid correspond to the conditions situated at “dangerous” regions of the phase diagram, i.e. near the critical temperature or close to the gas–liquid coexistence curve. The aim of present extensive simulations is to provide exact data for the broad range of the bulk parameters against which the “universality” of adjustable parameter associated with a perturbation density functional approximation (DFA) can be tested. Here the term “universality” means independence of this parameter on the particular external field responsible for the generation of a non-uniform density profile of the fluid. It is shown that the “universality” of this parameter associated with a third order+second order perturbation DFA holds also in the present case of a large spherical particle as a source of external potential, similarly as established in previous studies dealing with other interaction potential and other external fields [J. Chem. Phys., 122, 064503 (2005); J. Chem. Phys., 123 124708 (2005)]. This DFA can be used as input into a recently proposed framework for the calculation of interparticle potential of mean force (PMF).     

Dimanganese catalase—spectroscopic parameters from broken-symmetry density functional theory of the superoxidized MnIII/MnIV state

Broken-symmetry density functional theory was used to study the catalytic center of manganese catalase in the superoxidized Mn^III/Mn^IV state. Heisenberg exchange coupling constants, ⁵⁵Mn and ¹⁴N hyperfine coupling constants (hfcs) and nuclear quadrupole splittings, as well as the electronic g tensors were evaluated for different model systems of the active site after complete geometry optimizations in the high-spin and broken-symmetry states. A comparison of the experimental data with the spectroscopic parameters computed for the models with unprotonated and protonated -oxo bridges shows best agreement between theory and experiment for a Mn₂(-O)₂(-OAc) core. The calculated Mn–Mn distances and ⁵⁵Mn hfcs clearly support a dimanganese cluster with unprotonated -oxo bridges in the superoxidized state. Furthermore, it is shown that an interchange of the Mn^III and Mn^IV oxidation states in this trapped valence system leads to specific changes in the molecular and electronic structure of the manganese clusters.     

Structural analysis and the effect of cyclo(His–Pro) dipeptide on neurotoxins—a dynamics and density functional theory study

The switching propensity and maximum probability of occurrence of the side chain imidazole group in the dipeptide cyclo(His–Pro) (CHP) were studied by applying molecular dynamics simulations and density functional theory. The atomistic behaviour of CHP with the neurotoxins glutamate (E) and paraquat (Pq) were also explored; E and Pq engage in hydrogen bond formation with the diketopiperazine (DKP) ring of the dipeptide, with which E shows a profound interaction, as confirmed further by NH and CO stretching vibrational frequencies. The effect of CHP was found to be greater on E than on Pq neurotoxin. A ring puckering study indicated a twist boat conformation for the six-membered DKP ring. Molecular electrostatic potential (MESP) mapping was also used to explore the hydrogen bond interactions prevailing between the neurotoxins and the DKP ring. The results of this study reveal that the DKP ring of the dipeptide CHP can be expected to play a significant role in reducing effects such as oxidative stress and cell death caused by neurotoxins.     

Elucidation of insulin degrading enzyme catalyzed site specific hydrolytic cleavage of amyloid β peptide: a comparative density functional theory study

In this B3LYP study, the catalytic mechanisms for the hydrolysis of the three different peptide bonds (Lys28-Gly29, Phe19-Phe20, and His14-Gln15) of Alzheimer amyloid beta (Aβ) peptide by insulin-degrading enzyme (IDE) have been elucidated. For all these peptides, the nature of the substrate was found to influence the structure of the active enzyme–substrate complex. The catalytic mechanism is proposed to proceed through the following three steps: (1) activation of the metal-bound water molecule, (2) formation of the gem-diol intermediate, and (3) cleavage of the peptide bond. With the computed barrier of 14.3, 18.8, and 22.3 kcal/mol for the Lys28-Gly29, Phe19-Phe20, and His14-Gln15 substrates, respectively, the process of water activation was found to be the rate-determining step for all three substrates. The computed energetics show that IDE is the most efficient in hydrolyzing the Lys28-Gly29 (basic polar–neutral nonpolar) peptide bond followed by the Phe19-Phe20 (neutral nonpolar–neutral nonpolar) and His14-Gln15 (basic polar–neutral polar) bonds of the Aβ substrate.     

A density functional theory study of phenyl formation initiated by ethynyl radical (C2H•) and ethyne (C2H2)

An ab initio computational density functional theory (DFT) was used to study the formation of the first cyclic molecule (phenyl) initiated by the ethynyl radical (C₂H•). The study covers a competition reaction between the addition reactions of C₂H• with ethyne (C₂H₂) and some molecular re-arrangement schemes. The minimum energy paths of the preferred cyclic formation route were characterized. A thorough thermochemical analysis was performed by evaluating the differences in the energy of activation (ΔE), enthalpy (ΔH), and Gibb's free energy (ΔG) of the optimized stable and transition state (TS) molecules. The reaction temperatures were set to normal (T = 298 K) and combustion (T = 1,200 K) conditions.

Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study

A density functional theory study of the influence of the various functional groups of the molybdopterin ligand on electronic and geometric properties of active-site models for the molybdenum and tungsten cofactors has been undertaken. We used analogous molybdenum and tungsten complexes with increasingly accurate representation of the molybdopterin ligands and compared bond lengths, angles, charge distribution, composition of the binding orbitals, as well as the redox potentials in relation to each other. On the basis of our findings, we suggest using ligand systems including the pyrane and the pyrazine rings, besides the dithiolene function, to obtain sufficiently reliable computational, but also synthetic, models for the molybdenum and tungsten cofactors, whereas the second ring of the pterin might be neglected for efficiency reasons.     

Density functional theory,restricted Hartree–Fock simulations and vibrational spectroscopic studies of nicorandil

Fourier transform infrared and Raman spectra of nicorandil have been recorded. The structure, conformational stability, geometry optimisation and vibrational frequencies have been investigated. Complete vibrational assignments were made for the stable conformer of the molecule using restricted Hartree–Fock (RHF) and density functional theory (DFT) calculations (B3LYP) with the 6-31G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of the molecule and calculated results by RHF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. Natural bond order analysis of the title molecule was also carried out. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibration modes.     

Computational identification of RNA functional determinants by three-dimensional quantitative structure–activity relationships

Anti-infection drugs target vital functions of infectious agents, including their ribosome and other essential non-coding RNAs. One of the reasons infectious agents become resistant to drugs is due to mutations that eliminate drug-binding affinity while maintaining vital elements. Identifying these elements is based on the determination of viable and lethal mutants and associated structures. However, determining the structure of enough mutants at high resolution is not always possible. Here, we introduce a new computational method, MC-3DQSAR, to determine the vital elements of target RNA structure from mutagenesis and available high-resolution data. We applied the method to further characterize the structural determinants of the bacterial 23S ribosomal RNA sarcin–ricin loop (SRL), as well as those of the lead-activated and hammerhead ribozymes. The method was accurate in confirming experimentally determined essential structural elements and predicting the viability of new SRL variants, which were either observed in bacteria or validated in bacterial growth assays. Our results indicate that MC-3DQSAR could be used systematically to evaluate the drug-target potentials of any RNA sites using current high-resolution structural data.     

Performance of wave function and density functional methods for water hydrogen bond spin–spin coupling constants

Spin–spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob’s ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict ¹ J _{O H} , ² J _{H H} and ^2h J _{O O} couplings, while ^1h J _{O H} is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for ¹ J _{O H} and ² J _{H H} have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods.

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Graphical Abstract Evaluation of the additive effect of the hydrogen bond on spin-spin coupling constants of water using WF and DFT methods.