Computational approaches to shed light on molecular mechanisms in biological processes

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.     

Crystal and molecular structure of main adduct of benzaldoxime dehydrodimer and styrene

Three 1:1 adducts have been obtained by heating benzaldoxime dehydrodimer with styrene. The main product possesses the structure of bis-nitrone type. A radical addition mechanism is proposed.     

The crystal and molecular structure of the 2,4,6,8 tetra-t-Bu-phenothiazine 0.5 benzene adduct

The crystal structure of 2,4,6,8-tetra-t-Bu-phenothiazine 0.5C₆H₆ (Pnma space group, a=11.685, b=25.593, c=10.339) shows short intermolecular t-Bu(CH₃)Ph and CH₃CH₃ contacts which allow the formation of well defined channels along the a direction. These channels host one benzene molecule for each pair of phenothiazine molecules. AM1 molecular orbital calculations suggest that there is a strong coupling of the t-Bu groups rotations and the folding of the ring and this in turn makes the phenothiazine skeleton to be less folded than expected from the presence of four electron donating substituents.     

Assembling molecular species into 3D frameworks: Computational design and structure solution of hybrid materials

We present here the computational prediction of hybrid organic–inorganic extended lattices. The production of candidate crystal structures is successfully performed by direct-space assembly of building-units using the AASBU (Automated Assembly of Secondary Building Units) method, mixing independent organic and inorganic units. Hybrid candidates that are compatible with the imposed metal:organic ratio are generated with their cell parameters, space group, atomic positions, along with their simulated diffraction pattern. Since no explicit limit regarding the nature, number, and size of the inorganic and organic units, or hybrid building-block is involved, the method offers boundless potential for exploring hybrid frameworks in terms of the topological diversity. The most appealing development arises from the computer-assisted design of hybrid frameworks. Indeed, in a significant number of systems, it is well-known that controlled synthesis conditions can promote the occurrence of specific building-units, which serve to “propagate” the infinite crystal structure. We believe that the computational approach presented herein is valuable to create virtual libraries of viable hybrid polymorphs. We further show how it has proven to be, for the first time in the realm of hybrids, a tangible route towards structure solution in direct space, exemplified here with the computational structure determination of two complex hybrid structures, MIL-100 and MIL-101. This challenging area is of special interest when high quality diffraction data are not available or when very large cell sizes are involved. The development of a structural model in direct space, starting with minimal knowledge such as the metal:organic ratio, is shown here to be possible. With such a method in hand, formerly intractable structural problems when using methods based on conventional reciprocal space become feasible in direct space.     

Computational and experimental approaches for investigating membranes diffusion behavior in model diesel fuel

Genetic algorithms trained support vector regression predicting model is conducted to research diffusion behavior of methylnaphthalene and dibenzothiophene in four different membranes of polymethyl methacrylate, polymethyl acrylate, polyvinyl chloride and polyvinyl alcohol in model diesel fuel. It is found that the polyvinyl chloride is optimal membrane material for improving the diffusion selectivity of methylnaphthalene and dibenzothiophene, which demonstrates that the polyvinyl chloride membrane is favorable to the diesel fuel desulfurization. Also, molecular dynamic simulation is applied to validating the performance of genetic algorithm trained support vector regression model. The results of genetic algorithm trained support vector regression model reveal that the simulation values are well agreed with the experimental data and molecular dynamic simulation results. Meanwhile, the performance of the genetic algorithms trained support vector regression predict model is better than that of the genetic algorithms trained neural network model, which indicates that genetic algorithms trained support vector regression method offers a new prospected decision-theoretic approach to the diesel desulfurization.     

Crystal and molecular structure of aspartame X HCl X 2H2O

The crystal and molecular structure of the hydrochloride salt of the peptide sweetener aspartame (alpha-L-Asp-L-Phe methyl ester) has been determined at 120 K using 3877 reflections with I greater than 2.5 sigma I. Space group P2(1)2(1)2(1), cell dimensions a = 6.768(1), b = 9.796(1) and c = 26.520(3) A; final R factor 0.033. While the N-terminal L-Asp group in the structure of aspartame itself forms a six-membered ring with an intramolecular hydrogen bond between the carboxylate and the protonated amino terminus, the corresponding group in the hydrochloride adopts a completely different conformation with a weak intramolecular hydrogen bond between the carboxyl group and the N atom of the L-Phe residue. The L-Phe methyl ester moiety is rather similar in the two structures. Of the many possible conformations of aspartame, only one may be expected to function as a substrate at the receptor site for sweet taste, and a proposal is made for this active conformation.     

Computational approaches to design a molecular imprinted polymer for high selective extraction of 3,4-methylenedioxymethamphetamine from plasma

In this work, a molecular imprinted polymer (MIP) as a novel selective sorbent for extraction of 3,4-methylenedioxymethamphetamine (MDMA) from plasma samples was prepared. For selecting a more suitable monomer and polymerization solvent a methodology based on density functional theory calculations was developed. This computational design is based on the comparison of stabilization energies of the prepolymerization adducts between the template and different functional monomers. The effect of polymerization solvent was studied using of polarizable continuum model (PCM). The computational results revealed that the best suitable monomer and polymerization solvent for preparation of MIP is methacrylic acid (MAA) and chloroform, respectively. Also, another MIP with methacrylic acid (MAA) as monomer in acetonitrile was prepared to evaluate the validity of polarizable continuum model for selection of polymerization solvent. The performance of each polymer was evaluated by using Langmuir-Freundlich (LF) isotherm. As it is expected, the best results were obtained for the MIP which was prepared in chloroform. This MIP was used as a selective sorbent in solid-phase extraction coupled with high performance liquid chromatography-ultraviolet detector (MISPE-HPLC-UV) for rapid screening of MDMA in human plasma. For the proposed MISPE-HPLC-UV method, the linearity between responses (peak areas) and concentrations was found over the range of 3.6-11500 ng mL(-1) with a linear regression coefficient of 0.998. The limit of detection (LOD) and quantification (LOQ) in plasma were 1.0 and 3.3 ng mL(-1), respectively. The %RSD (n=5) data for five plasma samples containing 15, 25, 50, and 100 ng mL(-1) of MDMA were 1.02, 1.12, 2.05, 2.54, respectively.     

An experimental and theoretical study of the molecular structure and vibrational spectra of iodotrimethylsilane (SiIMe3)

The gas-phase molecular structure of iodotrimethylsilane (ITMS) has been determined from electron diffraction data. Infrared and Raman spectra have been completely assigned. The experimental work is supported by ab initio HF and MP2 calculations for the gas-phase structure determination and DFT(B3LYP) calculations, combined with Pulay's SQM method, for the vibrational spectra data.     

Crystal structure of the molecular adduct of antimony(III) fluoride with L-phenylalanine

The crystal structure of a newly synthesized molecular adduct of antimony(III) fluoride with L-phenylalanine of the composition SbF₃(C₉H₁₁NO₂) is determined for the first time (monoclinic crystal system: a = 5.8742(1) ?, b = 6.2079(1) ?, c = 15.5401(3) ?, β = 90.741(1)°, Z = 2, P2₁ space group). The structure consists of SbF₃ molecules and L-phenylalanine bound into polymer chains by bidentate bridging carboxyl groups of amino acid molecules. Weak Sb⋯F(3)^b bonds organize the adjacent chains into polymer ribbons that are bound into layers by N-H⋯F and N-H⋯O hydrogen bonds.     

From molecular clusters to liquid structure in AlCl3 and FeCl3

Melting of aluminum and iron trichloride is accompanied by a structural transition from sixfold to fourfold coordination of the trivalent metal ions, and a widely accepted interpretation of the structure of their melts near freezing is that they mainly consist of strongly correlated dimers formed from two edge-sharing tetrahedra. We carry out classical molecular dynamics simulations to examine how a polarizable-ion force law, determined on isolated molecular monomers and dimers in the gaseous phase of these compounds, fares in accounting for the pair structure of their liquid phase and for mean square displacements and diffusion coefficients of the two species in each melt. The model reproduces the main features of the neutron diffraction structure factor, showing peaks due to intermediate range order and to charge and density short-range order, and accounts for the experimental data at a good semi-quantitative level. We find agreement with the neutron and X-ray diffraction data on metal–halogen and Cl–Cl bond lengths in the melt, and demonstrate the high sensitivity of the results for the width of the first-neighbor shell to truncation in obtaining it by Fourier transform of the neutron-weighted structure factor in momentum space. We also report comparisons with a recent first-principles study of the structure of the AlCl₃ melt by the Car–Parrinello method. Finally, we demonstrate break-up of dimers into monomers upon raising the liquid temperature in the case of AlCl₃.     

Peroxo compounds: Part XVI. Electron diffraction investigation of the molecular structures of di-t-butyl peroxide Me3COOCMe3 and bis(trimethylsilyl) peroxide Me3SiOOSiMe3

The molecular geometries of Me₃COOCMe₃ and Me₃SiOOSiMe₃, in the gas phase were determined by electron diffraction. For the skeleton of di-t-butyl peroxide the following geometric parameters (r_a-values) were obtained: r(O—O) = 1.480 Å (assumed),

. This dihedral angle is compared with the results of IR and Ram an spectroscopy, dipole moment measurements and photoelectron spectroscopy. The main geometric parameters for bis(trimethylsilyl) peroxide are

. For both peroxides SCF-MO calculations in the CNDO/2 approximation do not reproduce the experimental results.     

Synthesis and quadratic molecular hyperpolarizabilities of two new chiral boronates: Computational and experimental study

A monomeric boronate and an oxobridged chiral dimer were obtained by reaction of the ligand derived from 4-diethylaminosalicylaldehyde with (R)-(−)-phenylglycinol, and phenyl boronic acid or boric acid. The compounds were fully characterized by spectroscopic techniques (¹H, ¹³C, ¹¹B NMR, elemental analyses, IR and masses spectrometry); and their molecular hyperpolarizabilities were investigated by the electric field induced second harmonic (EFISH) technique and semi-empirical calculations. The experimental quadratic hyperpolarizability which is equal to 9.8 × 10⁻³⁰ cm⁵ esu⁻¹ at 1.064 μm for the monomeric derivative rises to 19.5 × 10⁻³⁰ cm⁵ esu⁻¹ in the dimeric specie.     

Computational and experimental study of the mechanism of hydrogen generation from water by a molecular molybdenum-oxo electrocatalyst

We investigate the mechanism for the electrocatalytic generation of hydrogen from water by the molecular molybdenum-oxo complex, [(PY5Me(2))MoO](2+) (PY5Me(2) = 2,6-bis(1,1-bis(2-pyridyl)ethyl)pyridine). Computational and experimental evidence suggests that the electrocatalysis consists of three distinct electrochemical reductions, which precede the onset of catalysis. Cyclic voltammetry studies indicate that the first two reductions are accompanied by protonations to afford the Mo-aqua complex, [(PY5Me(2))Mo(OH(2))](+). Calculations support hydrogen evolution from this complex upon the third reduction, via the oxidative addition of a proton from the bound water to the metal center and finally an α-H abstraction to release hydrogen. Calculations further suggest that introducing electron-withdrawing substituents such as fluorides in the para positions of the pyridine rings can reduce the potential associated with the reductive steps, without substantially affecting the kinetics. After the third reduction, there are kinetic bottlenecks to the formation of the Mo-hydride and subsequent hydrogen release. Computational evidence also suggests an alternative to direct α-H abstraction as a mechanism for H(2) release which exhibits a lower barrier. The new mechanism is one in which a water acts as an intramolecular proton relay between the protons of the hydroxide and the hydride ligands. The calculated kinetics are in reasonable agreement with experimental measurements. Additionally, we propose a mechanism for the stoichiometric reaction of [(PY5Me(2))Mo(CF(3)SO(3))](+) with water to yield hydrogen and [(PY(5)Me(2))MoO](2+) along with the implications for the viability of an alternate catalytic cycle involving just two reductions to generate the active catalyst.