Computational study of formamide–water complexes using the SAPT and AIM methods

In this work, the complexes formed between formamide and water were studied by means of the SAPT and AIM methods. Complexation leads to significant alterations in the geometries and electronic structure of formamide. Intermolecular interactions in the complexes are intense, especially in the cases where the solvent interacts with the carbonyl and amide groups simultaneously. In the transition states, the interaction between the water molecule and the lone pair on the amide nitrogen is also important. In all the complexes studied herein, the electrostatic interactions between formamide and water are the main attractive force, and their contribution may be five times as large as the corresponding contribution from dispersion, and twice as large as the contribution from induction. However, an increase in the resonance of planar formamide with the successive addition of water molecules may suggest that the hydrogen bonds taking place between formamide and water have some covalent character.     

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.     

Structure of isolated tryptophyl-glycine dipeptide and tryptophyl-glycyl-glycine tripeptide: ab initio SCC-DFTB-D molecular dynamics simulations and high-level correlated ab initio quantum chemical calculations

The tryptophyl-glycine (Trp-Gly) and tryptophyl-glycyl-glycine (Trp-Gly-Gly) peptides have been studied by means of molecular dynamic simulations combined with high-level correlated ab initio quantum chemical and statistical thermodynamic calculations. The lowest energy conformers were localized in the free energy surface. The structures of the different Trp-Gly and Trp-Gly-Gly conformers coexisting in the gas phase have been for the first time reported and their scaled theoretical IR spectra unambiguously assigned and compared with previous gas-phase experimental results. Common geometrical features have been systematically observed for the sequence Trp, Trp-Gly, and Trp-Gly-Gly. In addition, the peptide backbone of Trp-Gly-Gly has been compared with that of the previously studied Phe-Gly-Gly (Reha, D. et. al. Chem. Eur. J. 2005, 11, 6803). From the observed systematic structural behavior between these peptide analogues, it is expected that the gas-phase conformers of other similar aromatic small peptides would present equivalent geometries. The DFT methodology failed to describe the potential energy surface of the studied peptides since the London dispersion energy (not covered in DFT) plays a significant role in the stabilization of most stable conformers.     

From the X-ray compact structure to the elongated form of the full-length MMP-2 enzyme in solution: a molecular dynamics study

Current understanding on the collagenolytic activity performed by the MMPs assumes some degree of relative motion between the catalytic and the hemopexin-like domains of the enzyme. However, all the crystal structures available for the full-length enzymes display a compact arrangement of the protein domains. Herein, we employ Molecular Dynamics simulations to investigate the structure of the full-length MMP-2 enzyme in aqueous solution. This simulation, together with previous experimental results that have been obtained very recently for the MMP-9 and MMP-12 enzymes, gives strong support to the hypothesis that the interdomain dynamics of the MMP enzymes in solution can result in a manifold of conformations including some structures with a large interdomain separation. The simulation of MMP-2 provides also a detailed molecular picture of the structures involved in the transition from the compact X-ray arrangement to the extended form in solution. Such information could be helpful in future studies of the regulation and/or the collagenolytic activity of these important enzymes.     

Use of beta-cyclodextrins to prevent modifications of the properties of carbopol hydrogels due to carbopol-drug interactions

Carbomers are carboxyvinylic derivatives that are widely used in the manufacture of hydrogel dosage forms. Because of their anionic nature and large number of acid groups, they tend to interact with cationic substances, and with other hydrophilic polymers containing alcohol groups. Here, we report a study of interactions between the carbomer Carbopol and the cationic drug propranolol hydrochloride in the solid state and in solution, and of the effects of such interactions on the properties of the hydrogel. We found that the drug forms an insoluble ionic complex with the polymer, modifying all of the hydrogel properties studied (swelling, release, bioadhesion). The inclusion of beta-cyclodextrin in the formulation reduces polymer/drug interactions, so that hydrogel properties remain unchanged. This is probably attributable to formation of inclusion complexes of beta-cyclodextrin and the drug, so that the drug is prevented from interacting with the polymer.     

Ketone–Alcohol Hydrogen‐Transfer Equilibria: Is the Biooxidation of Halohydrins Blocked?

To ensure the quasi‐irreversibility of the oxidation of alcohols coupled with the reduction of ketones in a hydrogen‐transfer (HT) fashion, stoichiometric amounts of α‐halo carbonyl compounds have been employed as hydrogen acceptors. The reason that these substrates lead to quasi‐quantitative conversions has been tacitly attributed to both thermodynamic and kinetic effects. To provide a clear rationale for this behavior, we investigate herein the redox equilibrium of a selected series of ketones and 2‐propanol by undertaking a study that combines experimental and theoretical approaches. First, the activity of the (R)‐specific alcohol dehydrogenase from Lactobacillus brevis (LBADH) with these substrates was studied. The docking of acetophenone/(R)‐1‐phenyethanol and α‐chloroacetophenone/(S)‐2‐chloro‐1‐phenylethanol in the active site of the enzyme confirms that there seems to be no structural reason for the lack of reactivity of halohydrins. This assumption is confirmed by the fact that the corresponding aluminum‐catalyzed Meerwein–Ponndorf–Verley–Oppenauer (MPVO) reactions afford similar conversions to those obtained with LBADH, showing that the observed reactivity is independent of the catalyst employed. While the initial rates of the enzymatic reductions and the IR ν(C?O) values contradict the general belief that electron‐withdrawing groups increase the electrophilicity of the carbonyl group, the calculated ΔG values of the isodesmic redox transformations of these series of ketones/alcohols with 2‐propanol/acetone support the thermodynamic control of the reaction. As a result, a general method to predict the degree of conversion obtained in the HT‐reduction process of a given ketone based on the IR absorption band of the carbonyl group is proposed, and a strategy to achieve the HT oxidation of halohydrins is also shown.     

The coercivities of mixtures of two ferromagnetic sponges in WC-Co cemented carbides

Evidence is presented to show that the coercive fields of mixtures of two ferromagnetic sponges behave according to the predictions of the Gerlach Principle for mixtures of two non-interacting systems of ferromagnetic particles. A consequence is that the behaviour of the coercive force of one of the sponges, although interconnected and interacting magnetostatically, is indistinguishable from that of a single system of non-interacting ferromagnetic particles. Only a knowledge of the internal demagnetising factors, the magnitudes of which influence the absolute magnitudes of the coercive fields, can distinguish the two systems. This conclusion is supported by further evidence that coercive fields of mixed ferromagnetic sponges are the same whether in contact, i.e. when short range interactions operate, or whether separated by 5 mm, i.e. when long range interactions operate. An experimental method for characterising component coercivities in mixtures of sponges is also presented.     

Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: experiment and theory

The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA) tripeptide was explored by molecular dynamics (MD) simulations in combination with high-level correlated ab initio quantum chemical calculations and metadynamics. Both the MD and metadynamics employed the tight-binding DFT-D method instead of the AMBER force field, which yielded inaccurate results. We classified the minima localised in the FESs as follows: a) the backbone-conformational arrangement; and b) the existence of a COOH...OC intramolecular H-bond (families CO(2)H(free) and CO(2)H(bonded)). Comparison with experimental results showed that the most stable minima in the FES correspond to the experimentally observed structures. Remarkably, however, we did not observe experimentally the CO(2)H(bonded) family (also predicted by metadynamics), although its stability is comparable to that of the CO(2)H(free) structures. This fact was explained by the former's short excited-state lifetime. We also carried out ab initio calculations using DFT-D and the M06-2X functional. The importance of the dispersion energy in stabilising peptide conformers is well reflected by our pioneer analysis using the DFT-SAPT method to explore the nature of the backbone/side-chain interactions.     

Fluorometric determination of serine in blood

A simple and rapid technique for the quantitative determination of serine in blood is presented. The method involves the removal of glucose in the protein-free filtrate and the oxidation of serine by periodate to formaldehyde. The latter is determined fluorometrically. Recovery studies of serine added to blood or plasma samples have been satisfactory.     

Chitosan Films Obtained from Brachystola magna (Girard) and Its Evaluation on Quality Attributes in Sausages during Storage

High molecular weight chitosan (≈322 kDa) was obtained from chitin isolated from Brachystola magna (Girard) to produced biodegradable films. Their physicochemical, mechanical and water vapor permeability (WVP) properties were compared against commercial chitosan films with different molecular weights. Brachystola magna chitosan films (CFBM) exhibited similar physicochemical and mechanical characteristics to those of commercial chitosans. The CFBM films presented lower WVP values (10.01 × 10⁻¹¹ g/m s Pa) than commercial chitosans films (from 16.06 × 10⁻¹¹ to 64.30 × 10⁻¹¹ g/m s Pa). Frankfurt-type sausages were covered with chitosan films and stored in refrigerated conditions (4 °C). Their quality attributes (color, weight loss, pH, moisture, texture and lipid oxidation) were evaluated at 0, 5, 10, 15 and 20 days. Sausages covered with CFMB films presented the lowest weight loss (from 1.24% to 2.38%). A higher increase in hardness (from 22.32 N to 30.63 N) was observed in sausages covered with CFMB films. Compared with other films and the control (uncovered sausages), CFMB films delay pH reduction. Moreover, this film presents the lower lipid oxidation level (0.10 malonaldehyde mg/sample kg). Thus, chitosan of B. magna could be a good alternative as packaging material for meat products with high-fat content.