Hyperfine coupling tensors of the benzosemiquinone radical anion from Car-Parrinello molecular dynamics.

Based on Car-Parrinello ab initio molecular dynamics simulations of the benzosemiquinone radical anion in both aqueous solution and the gas phase, density functional calculations provide the currently most refined EPR hyperfine coupling (HFC) tensors of semiquinone nuclei and solvent protons. For snapshots taken at regular intervals from the molecular dynamics trajectories, cluster models with different criteria for inclusion of water molecules and an additional continuum solvent model are used to analyse the HFCs. These models provide a detailed picture of the effects of dynamics and of different intermolecular interactions on the spin-density distribution and HFC tensors. Comparison with static calculations allows an assessment of the importance of dynamical effects, and of error compensation in static DFT calculations. Solvent proton HFCs depend characteristically on the position relative to the semiquinone radical anion. A point-dipolar model works well for in-plane hydrogen-bonded protons but deviates from the quantum chemical values for out-of-plane hydrogen bonding.     

Effect of temperature on the EPR properties of a rhamnose alkoxy radical: a DFT molecular dynamics study

It has been shown previously that two distinctive variants (called RHop and RO4) exist of the radiation-induced rhamnose alkoxy radical. Density functional theory (DFT) calculations of the electron paramagnetic resonance (EPR) properties were found to be consistent with two separate measurements at different temperatures [E. Pauwels, R. Declerck, V. Van Speybroeck, M. Waroquier, Radiat. Res., in press]. However, the agreement between theory and experiment was only of a qualitative nature, especially for the latter radical. In the present work, it is examined whether this residual difference between theoretical and experimental spectroscopic properties can be explained by explicitly accounting for temperature in DFT calculations. With the aid of ab-initio molecular dynamics, a temperature simulation was conducted of the RO4 variant of the rhamnose alkoxy radical. At several points along the MD trajectory, g and hyperfine tensors were calculated, yielding time (and temperature) dependent mean spectroscopic properties. The effect of including temperature is evaluated but found to be within computational error.     

Hyperfine interactions in aqueous solution of Cr3+: an ab initio molecular dynamics study

We performed an ab initio molecular dynamics simulation of the paramagnetic transition metal ion Cr³⁺ in aqueous solution. Isotropic hyperfine coupling constants between the electron spin of the chromium ion and nuclear spins of all water molecules have been determined for instantaneous snapshots extracted from the trajectory. The coupling constant of first sphere oxygen, A _iso(¹⁷O_I)=1.9±0.3 MHz, is independent on Cr–O_I distance but increases with the tilt angle for the water molecule approaching 180°. First sphere hydrogen spins have A _iso(¹ H_I)=2.1±0.2 MHz which decreases with increasing tilt angle and shows a Cr–H_I distance dependence. The hyperfine coupling constants for second sphere ¹⁷O is negative and an order of magnitude smaller (−0.20±0.02 MHz) compared to first sphere.     

Structures and EPR spectra of binary sulfur-nitrogen radicals from DFT calculations

The scattered electron paramagnetic resonance (EPR) spectroscopic data for binary sulfur-nitrogen (S,N) radicals have been compiled and critically assessed.Many of these are inorganic rings or cages.For each species, possible equilibrium structures in the gas phase and the EPR hyperfine coupling (hfc) constants have been calculated with DFT using the B3LYP functional and basis sets of triple-ζ (or better) quality.Good agreement is obtained between calculated and measured values for the well characterized [S₃N₂]⁺, a planar π-radical for which the s-component of the orbitals is likely to be reasonably independent of minor geometrical changes between gas-phase and condensed-phase states.The cage compounds [S₄N₄]⁻ and [S₄N₅]⁻², for which reliable experimental EPR spectra have been reported, show larger variation between calculated and measured hfc, as a consequence of the dependence of the s orbital content of the molecular orbitals on small structural changes.The very large disagreements between the DFT calculated and experimentally claimed hfc constants for [NS], [SNS] and [S₄N₄]⁻³ in condensed phases lead us to question their assignment.Among binary S,N radicals, ³³S hfc data has only been reported for [S₃N₂]⁺ (through isotopic enrichment).These values were essential for the correct identification of the EPR spectra of this important radical, which previously was misassigned to other species.Our results suggest that ³³S data will be equally important for the correct identification of the EPR spectra of other binary S,N species, many of which are cyclic systems, e.g.[S₃N₃], [S₄N₃] and[S₄N₅].     

Molecular dynamics simulations and quantum chemical calculations on β-cyclodextrin spironolactone complex

Molecular dynamics simulations on β-cyclodextrin in vacuo, with water and complexed with spironolactone (SP) were performed at a temperature of 300 K over a period of 1 ns. Two different orientations of SP in the cavity were considered. Along with conformational parameters, the formation of hydrogen bonds has been monitored during the whole simulation time. Cyclodextrins have the capability to form hydrogen bonds with the surrounding water molecules or intramolecular ones. The incorporation of ligands into the hydrophobic interior of β-cyclodextrin changes the preference of hydrogen bonds significantly and results in a contribution to the decrease of flexibility. Quantum chemical calculations on SP β-CD inclusion complex were performed to determine the interaction energy and to prove the applicability of various methods. Although all applied methods describe reasonable geometries for the association complex, higher level methods (e.g., B3LYP/6-31G(d,p)) seem to be necessary to determine reliable interaction energies.     

Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations.

A comparison of different treatments of bond-stretching interactions in molecular dynamics simulation is presented. Relative free energies from simulations using rigid bonds maintained with the SHAKE algorithm, using partially rigid bonds maintained with a recently introduced flexible constraints algorithm, and using fully flexible bonds are compared in a multi-configurational thermodynamic integration calculation of changing liquid water into liquid methanol. The formula for the free energy change due to a changing flexible constraint in a flexible constraint simulation is derived. To allow for a more direct comparison between these three methods, three different pairs of models for water and methanol were used: a flexible model (simulated without constraints and with flexible constraints), a rigid model (simulated with standard hard constraints), and an alternative flexible model (simulated with flexible constraints and standard hard constraints) in which the ideal or constrained bond lengths correspond to the average bond lengths obtained from a short simulation of the unconstrained flexible model. The particular treatment of the bonds induces differences of up to 2 % in the liquid densities, whereas (excess) free energy differences of up to 5.7 (4.3) kJ mol(-1) are observed. These values are smaller than the differences observed between the three different pairs of methanol/water models: up to 5 % in density and up to 8.5 kJ mol(-1) in (excess) free energy.     

Ab initio molecular orbital calculations of the infrared spectra of hydrogen-bonded complexes of water,ammonia and hydroxylamine

Summary The geometries of three hydrogen-bonded dimers of hydroxylamine have been optimized, at the MP2 level of theory, using the 6-31G** basis set. These calculations yielded three separate local minima on the dimer potential energy surface. The interaction energies of these three species have been calculated, and corrected for basis set superposition error. The infrared band wavenumbers and intensities have been computed, and the monomer-dimer wavenumber shifts and intensity enhancements rationalized in terms of the types and strengths of hydrogen bonds present. The predicted wavenumbers have been correlated with those measured in a recent matrix isolation spectroscopic study, and an argument for the structure of the preferred dimer has been presented.     

Ab initio molecular orbital calculations on ion pair-water complexes of metal halides and oxides

Ab initio MO calculations are performed on a series of ion-molecular and ion pair-molecular complexes of H₂O + MX (MX = LiF, LiCl, NaCl, BeO and MgO) systems. BSSE-corrected stabilization energies, optimized geometrical parameters, internal force constants and harmonic vibrational frequencies have been evaluated for all the structures of interest. The trends observed in the geometrical parameters and other properties calculated for the mono-hydrated contact ion pair complexes parallel those computed for the complexes of the individual ions. The bifurcated structures are found to be saddle points with an imaginary frequency corresponding to the rocking mode of water molecules. The solventshared ion pair complexes have high interaction energies. Trends in the internal force constant and harmonic frequency values are discussed in terms of ion-molecular and ion-pair molecular interactions.     

Dynamic structures of phosphodiesterase-5 active site by combined molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations

Various quantum mechanical/molecular mechanical (QM/MM) geometry optimizations starting from an x-ray crystal structure and from the snapshot structures of constrained molecular dynamics (MD) simulations have been performed to characterize two dynamically stable active site structures of phosphodiesterase-5 (PDE5) in solution. The only difference between the two PDE5 structures exists in the catalytic, second bridging ligand (BL2) which is HO- or H2O. It has been shown that, whereas BL2 (i.e. HO-) in the PDE5(BL2 = HO-) structure can really bridge the two positively charged metal ions (Zn2+ and Mg2+), BL2 (i.e. H2O) in the PDE5(BL2 = H2O) structure can only coordinate Mg2+. It has been demonstrated that the results of the QM/MM geometry optimizations are remarkably affected by the solvent water molecules, the dynamics of the protein environment, and the electronic embedding charges of the MM region in the QM part of the QMM/MM calculation. The PDE5(BL2 = H2O) geometries optimized by using the QM/MM method in different ways show strong couplings between these important factors. It is interesting to note that the PDE5(BL2 = HO-) and PDE5(BL2 = H2O) geometries determined by the QM/MM calculations neglecting these three factors are all consistent with the corresponding geometries determined by the QM/MM calculations that account for all of these three factors. These results suggest the overall effects of these three important factors on the optimized geometries can roughly cancel out. However, the QM/MM calculations that only account for some of these factors could lead to considerably different geometries. These results might be useful also in guiding future QM/MM geometry optimizations on other enzymes.     

EPR and IR spectral investigations on some leafy vegetables of Indian origin

EPR spectral investigations have been carried out on four edible leafy vegetables of India, which are used as dietary component in day to day life. In Rumex vesicarius leaf sample, EPR spectral investigations at different temperatures indicate the presence of anti-ferromagnetically coupled Mn(IV)–Mn(IV) complexes. EPR spectra of Trigonella foenum graecum show the presence of Mn ions in multivalent state and Fe³⁺ ions in rhombic symmetry. EPR spectra of Basella rubra indicate the presence of Mn(IV)–O–Mn(IV) type complexes. The EPR spectra of Basella rubra have been studied at different temperatures. It is found that the spin population for the resonance signal at g = 2.06 obeys the Boltzmann distribution law. The EPR spectra of Moringa oliefera leaves show the presence of Mn²⁺ ions. Radiation induced changes in free radical of this sample have also been studied. The FT-IR spectra of Basella rubra and Moringa oliefera leaves show the evidences for the protein matrix bands and those corresponding to carboxylic CO bonds.     

Folding behaviors of apocytochrome b5 and its mutants: Insights from high temperature molecular dynamics simulations

Apocytochrome b₅ (apocyt b₅) with heme removal from the heme-binding core 1, and its mutants with amino acid replaced in the hydrophobic core 2, namely apocyt b₅ Y7P, P81A and H15R/S20E, have been subjected to molecular dynamics (MD) simulation at high temperature (500 K) for elucidating their folding behaviors. The early events upon thermal induced unfolding were found to be in good agreement with available experimental results, and the lowest stability of Y7P was predicted among the four apoproteins. The influences of these key residues on protein folding behavior were compared directly at an atomic level. At the same time, the influences of non-native interactions of hydrogen bonds and salt-bridges on protein stabilities were analyzed in detail. The insights from current MD simulations are valuable for understanding the apoprotein folding and the holoprotein formation in terms of heme proteins.     

Structure and dynamics of high-spin Ru in aqueous solution: Ab initio QM/MM molecular dynamics simulation

The structural and dynamical properties of high-spin Ru²⁺ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru²⁺. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru²⁺ and the 6-31G^∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru²⁺–O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru²⁺ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.     

Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations

Polyglutamine (polyQ) diseases, including Huntington’s disease (HD), are caused by expansion of polyQ-encoding repeats within otherwise unrelated gene products. The aggregation mechanism of polyQ diseases, the inhibition mechanism of Congo red, and the alleviation mechanism of trehalose were proposed here based on quantum chemical calculations and molecular dynamics simulations. The calculations and simulations revealed the following. The effective molecular bonding is between glutamine (Gln) and Gln (Gln + Gln), between Gln and Congo red (Gln + Congo red), and between Gln and trehalose (Gln + trehalose). The bonding strength is −13.1 kcal/mol for Gln + Gln, −24.4 kcal/mol for Gln + Congo red, and −12.0 kcal/mol for Gln + trehalose. In the polyQ region, both the number of intermolecular Gln + Gln formations and the total calories generated by the Gln + Gln formation are proportional to the number of repetitions of Gln. We propose an aggregation mechanism whose heat generated by the intermolecular Gln + Gln formation causes the pathogeny of polyQ disease. In our aggregation mechanism, this generated heat collapses the host protein and promotes fibrillogenesis. Without contradiction, our mechanism can explain all the experimental results reported to date. Our mechanism can also explain the inhibition mechanism by Congo red as an inhibitor of polyglutamine-induced protein aggregation and the alleviation mechanism by trehalose as an alleviator of that aggregation. The inhibition mechanism by Congo red is explained by the strong interaction with Gln and by the characteristic structure of Congo red.     

Molecular dynamics simulations and free energy calculations on the enzyme 4‐hydroxyphenylpyruvate dioxygenase

4‐Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one‐step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

Toward <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> DXR inhibitor design: homology modeling and molecular dynamics simulations

Mycobacterium tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase (MtDXR) is a potential target for antitubercular chemotherapy. In the absence of its crystallographic structure, our aim was to develop a structural model of MtDXR. This will allow us to gain early insight into the structure and function of the enzyme and its likely binding to ligands and cofactors and thus, facilitate structure-based inhibitor design. To achieve this goal, initial models of MtDXR were generated using MODELER. The best quality model was refined using a series of minimizations and molecular dynamics simulations. A protein–ligand complex was also developed from the initial homology model of the target protein by including information about the known ligand as spatial restraints and optimizing the mutual interactions between the ligand and the binding site. The final model was evaluated on the basis of its ability to explain several site-directed mutagenesis data. Furthermore, a comparison of the homology model with the X-ray structure published in the final stages of the project shows excellent agreement and validates the approach. The knowledge gained from the current study should prove useful in the design and development of inhibitors as potential novel therapeutic agents against tuberculosis by either de novo drug design or virtual screening of large chemical databases. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Crystal structure and single crystal EPR of (NH4)2(15-crown-5)3[Cu(mnt)2] and (NH4)2(benzo-15-crown-5)4[Cu(mnt)2]·0.5H2O

The X-ray crystal structures of (NH4)2(15-crown-5)3[Cu(mnt)2] (1) and (NH4)2(benzo-15-crown-5)4- [Cu(mnt)2]·0.5H2O (2) were determined. Two single crystals are composed of distinct structures of ammonium-crown ether supramolecular cation and [Cu(mnt)2]2- anion. The triple-decker dication in complex 1 and a sandwich dimmer in complex 2 were observed. X-Band EPR studies on the single crystals of both complex 1 and complex 2 have been carried out at room temperature, which revealed that complex 2 showed a perfect hyperfine structure of Cu whereas that of complex 1 could not be observed. The principal values and direction cosines of the principal axes of the g and A tensors were computed by a least-squares fitting procedure. The spin density of Cu(Ⅱ) was estimated according to the principal values of the A tensors and compared well with the results calculated based on DFT method.     

Non empirical quantum mechanical calculations of the1H,13C,15N and17O magnetic shielding constants and of the spin-spin coupling constants in formamide,hydrated formamide and N-methylformamide

The magnetic shielding constants of the different atoms of formamide, hydrated formamide and N-methylformamide are calculated by anab initio method. For the protons of formamide the measured differences between their chemical shifts are correctly reproduced by theory, provided that the molecular geometry used as input is carefully chosen. The differences between the values of the magnetic shielding constants calculated for formamide and hydrated formamide show that intermolecular hydrogen bonding produces variations of chemical shifts for all the atoms of the molecule except the formyl proton. The calculated chemical shift variations between formamide and N-methylformamide are compared to the experimental values and discussed in relation with different hydrogen bonding possibilities of the two molecules. The calculation of the contact term of the spin-spin coupling constants of formamide and hydrated formamide shows that in most cases the measured trends are satisfactorily reproduced and that the variations of these terms upon hydration are less than 3%.     

Effects of water on epoxy cure kinetics and glass transition temperature utilizing molecular dynamics simulations

Effects of water on epoxy cure kinetics are investigated. Experimental tests show that absorbed water in an uncured bisphenol‐F/diethyl‐toluene‐diamine epoxy system causes an increase in cure rate at low degrees of cure and a decrease in cure rate at high degrees of cure. Molecular simulations of the same epoxy system indicate that the initial increase in cure rate is due to an increase in molecular self‐diffusion of the epoxy molecules in the presence of water. Effects of water on the glass transition temperature (T_g) of the crosslinked thermoset are also studied. Both experiments and simulations show that water decreases T_g. Both types of results indicate that T_g effects are small below 1% water by weight, but that T_g depression occurs much quickly with increasing water content above 1%. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1150–1159     

Ab initio calculations on large molecules using molecular fragments. Characterization of the zwitterion of glycine

The ab initio molecular fragment approach is applied to a characterization study of the ground state of the zwitterion of glycine. Included among the properties studied are the — conformational energy surface, the electronic structure, and the magnitude and direction of the dipole moment. The results of the present study are compared to the results of other theoretical and experimental studies.This work was supported in part by the National Science Foundation, the University of Kansas, and the Upjohn Company, Kalamazoo, Michigan 49001.NSF Trainee (1969-1972).Alfred P. Sloan Research Fellow (1971–1973).