Characterisation and causal model of the holistic dynamics of the integral sustainability of the agri-food system.

The transformation of the food and industrial agricultural production system into adaptative and sustainable systems capable of being productive within social, environmental, and economic limits is a crucial factor in reducing the risk to food security and to economic growth. However, the analysis structure of the effect of these variables in sustainable environments remains unknown, whereby the technology and processes are considered as variables of the equivalent critical level as those already described. The purpose of this study is to design a model that enables the characterisation of the agri-food sector based on the determination of sustainable variables from a sustainable and integral systemic approach. Tools, such as the viable system model, are employed to analyse the dynamics and generate the balanced scorecard, to which the items of learning and continuous improvement are added. Lastly, the impact of the principles of sustainability versus the variation of sustainability in the agri-food system is revealed, which is useful in determining the appropriate levels to guarantee a balance in the foundations of circularity. From a systemic approach, this model can be adopted by agronomists and scientists to design alternative strategies for the management of food sustainability.

Characterization of the information system integrated to the construction project management systems.

The construction industry wields significant influence in the economies of various countries. However, compared to sectors like manufacturing and aeronautics, it has lagged in terms of digitalization of processes and project management advancement. This study aims to explore how the integration of Lean principles, Building Information Modeling (BIM), and Project Lifecycle Management methodologies within an information system can enhance decision-making in construction project management as a complex environment. A comprehensive literature review was conducted to establish a conceptual framework and gather necessary information for designing an information system. The design was based on the viable systems model and the soft systems methodology, from a systemic perspective that encourages the synergistic interaction of these methodologies. The resulting abstract model would facilitate a comprehensive understanding of the interconnectedness of these methodologies, emphasizing collaborative work environments for efficient information management. This approach aims to replace the current isolated application of each of those methodologies and promises improved project management performance.

CADMA-Chem: A Computational Protocol Based on Chemical Properties Aimed to Design Multifunctional Antioxidants.

A computational protocol aimed to design new antioxidants with versatile behavior is presented. It is called Computer-Assisted Design of Multifunctional Antioxidants and is based on chemical properties (CADMA-Chem). The desired multi-functionality consists of in different methods of antioxidant protection combined with neuroprotection, although the protocol can also be used to pursue other health benefits. The dM38 melatonin derivative is used as a study case to illustrate the protocol in detail. This was found to be a highly promising candidate for the treatment of neurodegeneration, in particular Parkinson's and Alzheimer's diseases. This also has the desired properties of an oral-drug, which is significantly better than Trolox for scavenging free radicals, and has chelates redox metals, prevents the ●OH production, via Fenton-like reactions, repairs oxidative damage in biomolecules (lipids, proteins, and DNA), and acts as a polygenic neuroprotector by inhibiting catechol-O-methyl transferase (COMT), acetylcholinesterase (AChE) and monoamine oxidase B (MAOB). To the best of our best knowledge, CADMA-Chem is currently the only protocol that simultaneously involves the analyses of drug-like behavior, toxicity, manufacturability, versatile antioxidant protection, and receptor-ligand binding affinities. It is expected to provide a starting point that helps to accelerate the discovery of oral drugs with the potential to prevent, or slow down, multifactorial human health disorders.

Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations.

Sulfonamides are an important class of therapeutic agents. The increase in the number of new sulfonamide derivatives makes it necessary to study more rationally the chemical structure, because the solid forms often display different mechanical, thermal and physicochemical properties that can influence the bioavailability and stability of the drugs; consequently, the polymorphic structures are of great interest to the pharmaceutical industry because of their ability to modify the physical properties of the active pharmaceutical ingredient. The molecular interactions of these drugs in their crystal lattice are important for the stability of the crystals and polymorphism and for preparing composite complexes for optimizing the use of these drugs. In this work, the crystal structure of these drugs and crystal polymorphism is investigated. So, the crystal forms of antibiotics derivatives of the sulfonamides, sulfamethoxazole, sulfamethazine, sulfachloropyridazine, and sulfacetamide are studied at the molecular and supramolecular level by using computational modeling approach at quantum mechanical level. The spectroscopic properties of these systems are also studied explaining assignments of previous experimental data. The results of DFT calculations reproduce the crystal structures of sulfonamides determined experimentally and the polymorphism in these molecules have been clarified. Likewise, the main intermolecular interactions in all crystal forms of these sulfonamides are H-bonds among the sulfonic and amino groups and SNH groups, and also some π-π interactions. Also, these 3-D periodical models allow the exploration of the intermolecular interactions included in the crystal structures and some of these interactions can alter the vibration modes of the molecules. Therefore, the use of these models can be useful for experimental spectroscopy studies where use actual crystal solids.

Detailed Investigation of the Outstanding Peroxyl Radical Scavenging Activity of Two Novel Amino-Pyridinol-Based Compounds.

The ability of two novel amino-pyridinol based compounds (NPyr6 and NPyr7) as peroxyl radical scavengers was investigated in silico. The gathered data indicate that they are exceptionally efficient in that role. However, solvent polarity influences their relative efficiency for that purpose. NPyr6 was identified as the best peroxyl radical scavenger in lipid solution, while NPyr7 takes that place in aqueous solution. Both compounds present two acid-base equilibria, which influence their reactivity in aqueous solution. The associated pKa values were estimated. Several reaction mechanisms were explored. Hydrogen transfer from the phenolic group was identified as the chemical route with the highest contribution to the antioxidant behavior of the investigated compounds in both, nonpolar medium and aqueous solution (at 2 ≤ pH ≤ 10). At higher pH other reaction pathways become the most relevant ones. In addition, their bioavailability, cell permeability, safety, and manufacturability were evaluated. According to these, particularly toxicity, NPyr7 seems to be a better candidate for use as an oral drug to fight oxidative stress than NPyr6.

The reactions of plant hormones with reactive oxygen species: chemical insights at a molecular level.

The reactions of two plant hormones, namely jasmonic acid (JA) and methyl jasmonate (MJ), with different reactive oxygen species (ROS) were investigated using the density functional theory. Different reaction sites and mechanisms were explored, as well as solvents of different polarity, and pH in aqueous solution. The thermochemical viability and kinetics of the investigated reaction pathways were found to be strongly influenced by the reacting ROS. All the investigated pathways were found to be exergonic, both in aqueous and lipid solution and for both JA and MJ, when the reactions involve •OH and •OCH3. On the contrary, for the reactions with peroxy radicals (•OOH and •OOCH2CHCH2) only a few hydrogen transfer pathways were found to be thermochemically viable. The reactions involving •OH were found to be diffusion-controlled, with both JA and MJ, regardless of the polarity of the solvent. This led to the hypothesis that the direct •OH scavenging activity of JA and MJ might play a role in the beneficial effects of the jasmonate family regarding the antioxidant defense of plants against metal-induced oxidative stress. The deprotonated fraction of JA is, to some extent, more reactive than the neutral fraction toward ROS. This, together with the acid-base equilibria inherent to some ROS, make the pH an influential environmental factor on the overall reactivity of JA toward ROS.

Computational study of substituent effects on the acidity, toxicity and chemical reactivity of bacteriostatic sulfonamides.

Relationships among physicochemical properties, the chemical structure and antibacterial activity of sulfonamides have not been completely explicated yet. Nevertheless, from a therapeutics and prodrugs design point of view, a substituent group can modify the electronic structure, the physicochemical features and chemical reactivity which are critical for the biological activity. In this work, we analyze the substituent effects on the physicochemical properties, toxicity, chemical reactivity and its relation with the bacteriostatic activity of selected sulfonamides by means of DFT-M06-2X calculations in aqueous solution, using quantum chemical and docking descriptors. A correlation between the theoretical acidity and the pKa experimental values has been found. The more active sulfonamides have a larger acidity. The acidity increases with electron-withdrawing substituents. The main reactivity takes place on N4 atoms linked to aromatic ring, and in the SO2NH moiety, which are influenced by substituents. Docking descriptors showed binding affinities between sulfonamides and target receptor, the dihydropteroate synthase (DHPS).

Polymorphism, Intermolecular Interactions, and Spectroscopic Properties in Crystal Structures of Sulfonamides.

The antibiotics family of sulfonamides has been used worldwide intensively in human therapeutics and farm livestock during decades. Intermolecular interactions of these sulfamides are important to understand their bioactivity and biodegradation. These interactions are also responsible for their supramolecular structures. The intermolecular interactions in the crystal polymorphs of the sulfonamides, sulfamethoxypyridazine, and sulfamethoxydiazine, as models of sulfonamides, have been studied by using quantum mechanical calculations. Different conformations in the sulphonamide molecules have been detected in the crystal polymorphs. Several intermolecular patterns have been studied to understand the molecular packing behavior in these antibiotics. Strong intermolecular hydrogen bonds and π-π interactions are the main driving forces for crystal packing in these sulfonamides. Different stability between polymorphs can explain the experimental behavior of these crystal forms. The calculated infrared spectroscopy frequencies explain the main intermolecular interactions in these crystals.

On the chemical behavior of C60 hosting H2O and other isoelectronic neutral molecules.

The density functional theory (DFT) was used to investigate the chemical behavior of C60 hosting neutral guest molecules (NGM). The deformed atoms in molecules (DAM) allowed identifying the regions of electron density depletion and accumulation. The studied NGM are CH4, NH3, H2O, and HF. Based on dipole moment and polarizabilities analyses it is predicted that the NGM@C60 should be more soluble in polar solvents than C60. The deformations on the surface electron density of the fullerenes explain this finding, which might be relevant for further applications of these systems. It was found that the intrinsic reactivity of studied NGM@C60 is only moderately higher than that of C60. This trend is supported by the global reactivity indexes and the frontier orbitals analyses. The free radical scavenging activity of the studied systems, via single electron transfer, was found to be strongly dependent on the chemical nature of the reacting free radical. The presence of the studied NGM inside the C60 influences only to some extent the reactivity of C60 toward free radicals. The distortion of the electron density on the C60 cage, caused by the NGM, is directly related to the electron withdrawing capacity of the later.

Ellagic acid: an unusually versatile protector against oxidative stress.

Several aspects related to the antioxidant activity of ellagic acid were investigated using the density functional theory. It was found that this compound is unusually versatile for protecting against the toxic effects caused by oxidative stress. Ellagic acid, in aqueous solution at physiological pH, is able of deactivating a wide variety of free radicals, which is a desirable capability since in biological systems, these species are diverse. Under such conditions, the ellagic acid anion is proposed as the key species for its protective effects. It is predicted to be efficiently and continuously regenerated after scavenging two free radicals per cycle. This is an advantageous and unusual behavior that contributes to increase its antioxidant activity at low concentrations. In addition, the ellagic acid metabolites are also capable of efficiently scavenging a wide variety of free radicals. Accordingly, it is proposed that the ellagic acid efficiency for that purpose is not reduced after being metabolized. On the contrary, it provides continuous protection against oxidative stress through a free radical scavenging cascade. This is an uncommon and beneficial behavior, which makes ellagic acid particularly valuable to that purpose. After deprotonation, ellagic acid is also capable of chelating copper, in a concentration dependent way, decreasing the free radical production. In summary, ellagic acid is proposed to be an efficient multiple-function protector against oxidative stress.

Crystal structure, stability and spectroscopic properties of methane and CO2 hydrates.

Methane hydrates are highly present in sea-floors and in other planets and their moons. Hence, these compounds are of great interest for environment, global climate change, energy resources, and Cosmochemistry. The knowledge of stability and physical-chemical properties of methane hydrate crystal structure is important for evaluating some new green becoming technologies such as, strategies to produce natural gas from marine methane hydrates and simultaneously store CO2 as hydrates. However, some aspects related with their stability, spectroscopic and other chemical-physical properties of both hydrates are not well understood yet. The structure and stability of crystal structure of methane and CO2 hydrates have been investigated by means of calculations with empirical interatomic potentials and quantum-mechanical methods based on Hartree-Fock and Density Functional Theory (DFT) approximations. Molecular Dynamic simulations have been also performed exploring different configurations reproducing the experimental crystallographic properties. Spectroscopic properties have also been studied. Frequency shifts of the main vibration modes were observed upon the formation of these hydrates, confirming that vibration stretching peaks of C-H at 2915cm(-1) and 2905cm(-1) are due to methane in small and large cages, respectively. Similar effect is observed in the CO2 clathrates. The guest-host binding energy in these clathrates calculated with different methods are compared and discussed in terms of adequacy of empirical potentials and DFT methods for describing the interactions between gas guest and the host water cage, proving an exothermic nature of methane and CO2 hydrates formation process.

Physicochemical insights on the free radical scavenging activity of sesamol: importance of the acid/base equilibrium.

Reactions of sesamol with different free radicals, in lipid and aqueous media, have been studied at the M05-2X/6-311+G(d,p) level of theory in conjunction with the SMD continuum model. Different mechanisms of reaction have been considered as well as polar and nonpolar environments. According to the overall rate coefficients, sesamol is predicted to react significantly faster in aqueous solution than in nonpolar media. The polarity of the environment also changes the relative importance of the reaction mechanisms. The anionic form of sesamol was found to be particularly reactive toward peroxyl radicals by transferring one electron. This mechanism was found responsible for the exceptional peroxyl radical scavenging activity of sesamol in aqueous solution, which was found to be even better than carotenoids, 2-propenesulfenic acid, and glutathione under physiological conditions. The agreement between experimental and calculated data supports the presented results as well as the methodology used in this work.

Canolol: a promising chemical agent against oxidative stress.

The OOH radical scavenging activity of canolol (CNL) has been studied in aqueous and lipid solutions, using the density functional theory. CNL is predicted to react about 3.6 times faster in aqueous solution than in lipid media. The overall rate coefficients are predicted to be 2.5 × 10(6) and 6.8 × 10(5) M(-1) s(-1), respectively. The OOH radical scavenger activity of canolol is predicted to be similar to that of carotenes, higher than that of allicin, and much higher than that of melatonin. Branching ratios for the different channels of reaction are reported for the first time. It was found that the reactivity of canolol toward OOH radicals takes place almost exclusively by H atom transfer from the phenolic moiety in canolol, regardless of the polarity of the environment. Taking into account that the reactivity of peroxyl radicals is significantly lower than that of other reactive oxygen species, canolol is proposed to be a very good antioxidant.

Mechanism and kinetics studies on the antioxidant activity of sinapinic acid.

The OOH radical scavenging activity of sinapinic acid (HSA) has been studied in aqueous and lipid solutions, using the Density Functional Theory. HSA is predicted to react about 32.6 times faster in aqueous solution than in lipid media. The overall rate coefficients are predicted to be 5.39 × 10(5) and 1.66 × 10(4) M(-1) s(-1), respectively. Branching ratios for the different channels of reaction are also reported for the first time, as well as the UV-Vis spectra of the main products of reaction. It was found that the reactivity of sinapinic acid towards OOH radicals takes place almost exclusively by H atom transfer from its phenolic moiety. However it was found to react via SET, at diffusion-limit controlled rate constants, with ˙OH, ˙OCCl(3) and ˙OOCCl(3) radicals. It was found that the polarity of the environment and the deprotonation of HSA in aqueous solution, both increase the reactivity of this compound towards peroxyl radicals.

Mechanism and branching ratios of hydroxy ethers + (*)OH gas phase reactions: relevance of h bond interactions.

A theoretical study on the mechanism and branching ratios of the gas phase reactions of hydroxyl radicals with a series of hydroxy ethers is presented. This is the first report on branching ratios for these reactions. The studied hydroxy ethers are: methoxy-methanol (MM), ethoxy-methanol (EM), 1-methoxy-ethanol (1ME), 2-methoxy-ethanol (2ME), and 2-ethoxy-ethanol (2EE). All the possible H abstraction channels have been modeled, involving the rupture of C-H and O-H bonds. The H abstractions from the alcohol group were found to be almost negligible for all the studied systems. The role of H bond interactions in the transition states (TS) is discussed, as well as the importance of the location of the reaction site with respect to the alcohol and the ether functional groups. TSs with seven-member ring-like structures were found to lead to stronger H bond interactions than TSs with six- and five-member ring-like structures, with the latter leading to the weakest interactions. Kinetic calculations have been performed within the 250-440 K temperature range. Rate coefficients for the reactions of (*)OH with MM, EM, and 1ME are reported here for the first time. Nonlinear Arrhenius plots were found for all the overall reactions. Negative activation energies at room temperature are proposed for the (*)OH reactions with EM, 2ME, and 2EE. The excellent agreement with the scarce experimental data available supports the reliability of the data reported here for the first time.

Water complexes of important air pollutants: geometries, complexation energies, concentrations, infrared spectra, and intrinsic reactivity.

Water complexes involving methanol, ethanol, formaldehyde, formic acid, acetone, ammonia, acetylene, ethylene, chloroethene, trichloroethene, 1,1,1-trichloroethane, hydroxyl radical, and hydroperoxyl radical have been studied. Enthalpies, entropies, and Gibbs free energies of association have been estimated, as well as the concentrations of the complexes under lower-troposphere conditions. The influence of the relative air humidity on the complexation processes has been analyzed. The association processes yielding water complexes of methanol, ethanol, formic acid, ammonia, acetone, hydroxyl radical, and hydroperoxyl radical were found to be more exothermic than that of the water dimer. General trends for the reactivity of the studied water complexes, compared to those of the corresponding free species, are proposed based on global reactivity indexes. The previously reported increased reactivity of the (*)OOH self-reaction, when there is water present, has been explained. The IR spectra of the complexes have been analyzed and compared with those of the free species.

Peroxyl-radical-scavenging activity of garlic: 2-propenesulfenic acid versus allicin.

The OOH radical reactions with allicin and its Cope elimination products (2-propenesulfenic acid and thioacrolein) in aqueous solution have been studied. The CBS-QB3 quantum chemistry method has been used, with geometries and frequencies at BHandHLYP/6-311++G(d,p) level and conventional transition state theory. 2-Propenesulfenic acid is predicted to be over 1000 times more reactive toward OOH radical than allicin (2.60 x 10(7) vs 7.38 x 10(3) L mol(-1) s(-1), at 298 K). Accordingly, our results strongly support the novel suggestion by Vaidya et al. (Angew. Chem., Int. Ed. 2009, 48, 157) that the active ingredient responsible for the free radical scavenging activity of garlic is actually 2-propenesulfenic acid and not allicin. In addition, direct reaction branching ratios and product distribution for the three studied reactions are proposed for the first time.

Reactions of OOH radical with beta-carotene, lycopene, and torulene: hydrogen atom transfer and adduct formation mechanisms.

The relative free radical scavenging activity of beta-carotene, lycopene, and torulene toward OOH radicals has been studied using density functional theory. Hydrogen atom transfer (HAT) and radical adduct formation (RAF) mechanisms have been considered. All the possible reaction sites have been included in the modeling, and detailed branching ratios are reported for the first time. The reactions of hydrocarbon carotenoids (Car) with peroxyl radicals, in both polar and nonpolar environments, are predicted to proceed via RAF mechanism, with contributions higher than 98% to the overall OOH + Car reactions. Lycopene and torulene were found to be more reactive than beta-carotene. In nonpolar environments the reactivity of the studied carotenoids toward peroxyl radical follows the trend LYC > TOR > BC, whereas in aqueous solutions it is TOR > LYC > BC. OOH adducts are predicted to be formed mainly at the terminal sites of the conjugated polyene chains. The main addition sites were found to be C5 for beta-carotene and lycopene and C30 for torulene. The general agreement between the calculated magnitudes and the available experimental data supports the predictions from this work.

Role of the sulfur atom on the reactivity of methionine toward OH radicals: comparison with norleucine.

Density functional theory has been used to model the OH reaction with Gly-Met-Gly and Gly-Nle-Gly tripeptides. The first one is predicted to be about 100 times faster than the second one. Therefore, if a methionine fragment is replaced by norleucine, the overall reactivity of the peptide toward free radicals is expected to be significantly reduced, which is in agreement with previous experimental findings. Since the most reactive sites were found to be located in the central backbone for Nle and in the terminal fragment of the side chain for Met, this decrease is expected to be even more critical for large-sized free radicals. The S atom seems to activate not only those alkyl sites next to it but also those located an odd number of bonds apart. In addition the viability of different paths explaining the formation of methionine sulfoxide has been tested, and it is proposed that this process involves the formation of R-SO radical and formaldehyde. The results from the present work offer an explanation to the role of sulfur atom on the reactivity of methionine toward free radicals. They also support the preponderant role of Met35 on the development of the Alzheimer disease.

A possible mechanism for furan formation in the tropospheric oxidation of dienes.

The isoprene + OH gas-phase reaction has been widely studied because of its relevance in tropospheric chemistry. However, an unsolved question remains concerning the mechanism for the formation of the observed 3-methylfuran. OH addition to dienes, such as isoprene and butadiene, is assumed to occur only at the external carbon atoms, thus restricting furan formation to a step after addition at C1 and C4. Moreover, cyclization of the carbon chain necessarily involves a cis conformation. In this work, several quantum chemistry methods have been used to model five different reaction paths for furan formation. A mechanism that is highly favored for intermediates that do not undergo collisional stabilization has been identified.