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Among many theories on the life's origins, the regions between star systems in a galaxy are hypothesized to provide prebiotic material on Earth. Simple sugars, including glycolaldehyde, are confirmed to exist in interstellar medium (ISM) and can be intermediates in the formose reaction to form dihydroxyacetone (DHA). In the studied segment of the formose reaction, hydroxy carbene is sequentially added to formaldehyde, forming glycolaldehyde (hydroxyacetaldehyde) after the first addition and glycerone in the second addition. The proposed theoretical mechanism was validated through quantum chemical calculations. An exothermic and exergonic pathway favourable in ISM conditions was found, giving a possible explanation for glycerone formation. The products in question participate in biological processes like energy production, the phosphorylated form of glycerone (DHA-P) participates in glycolysis, and energy storage while glycerone is the source of the glycerine backbone in lipids. The studied reaction is a segment of the formose reaction and further polymerization can lead to pentose and hexose, which participate in the formation of RNA and DNA. Hence, this research explores the exogenous production and delivery of prebiotic material to Earth, building up to the conditions allowing the formation of rudimentary lifeforms. Key words: astrochemistry, hydroxy carbene, interstellar medium, computational chemistry, formose reaction. Parmi de nombreuses theories sur les origines de la vie, on suppose que la matière prebiotique sur Terre proviendrait de regions entre les systèmes stellaires d'une galaxie. La presence de sucres simples, notamment le glycolaldehyde, dans le milieu interstellaire (MI) a ete confirmee, et ceux-ci peuvent intervenir dans la reaction de formose pour former la dihydroxyacetone (DHA). Dans le segment de la reaction de formose que nous avons etudie, l'hydroxycarbène est ajoute de manière sequentielle au formaldehyde, pour former le glycolaldehyde (hydroxyacetaldehyde) après l'addition d'une première unite, et la glycerone après l'addition d'une seconde. Le mecanisme theorique propose a ete valide par des calculs de chimie quantique. Nous avons decouvert une voie exothermique et exergonique favorable dans des conditions de MI qui pourrait expliquer la formation de glycerone. Les produits en question sont impliques dans des processus biologiques comme la production d'energie : la forme phosphorylee de la glycerone, la DHAP, participea la glycolyse et au stockage d'energie, tandis que la glycerone sert de precurseur au squelette glycerol dans les lipides. La reaction etudiee est un segment de la reaction de formose qui, lorsqu'elle se poursuit par une polymerisation, peut produire des pentoses et des hexoses participanta la formation de l'ARN et de l'ADN. Par consequent, cette recherche explore l'hypothèse de la production exogène de matière prebiotique et de son arrivee sur Terre pour s'y assembler progressivement dans des conditions permettant l'emergence de formes de vie rudimentaires. [Traduit par la Redaction] Mots-cles : astrochimie, hydroxycarbène, milieu interstellaire, chimie computationnelle, reaction de formose., Introduction From the very first microorganisms that were able to flourish in the harsh environment of early Earth, to the astounding diversity and complexity of today's lifeforms, life as we [...]

Finding a relationship on how a three-dimensional protein folds from its linear amino acid chain gets more complex with increasing chain length, so working on a smaller peptide conformational problem can provide initial ideas on what are the main molecular forces and how these influence the folding process. Following the study of conformations of amino acid units entering the proteins to understand the secondary structure of small peptides, this paper proposes mathematical models for the several two-rotor cross-sections of the five-dimensional N-acetyl-glycyl-glycine-N'-methylamide potential energy hypersurface (PEHS). These cross-sections are extracted along the first glycine subunit, with its coordinates fixed at the five energy minima of the glycine diamide. The resulting mathematical models yield an average RMSE of 1.36 kJ [mol.sup.-1] and an average [R.sup.2] of 0.9923 with respect to energy values obtained from DFT calculations. The minima geometries obtained from these models are also in good agreement with DFT-optimized energy minima conformers. An important aspect of this study also tackles the relationship between the PEHS of the glycyl-glycine diamide and its glycine subunits. It has been observed that there are deviations up to 28.35 kJ [mol.sup.-1] and 29.52 kJ [mol.sup.-1] between the PEHS cross-sections along [[gamma].sub.L] and [[gamma].sub.D] conformations, respectively, in the first glycine subunit. This may suggest that there are significant backbone-backbone intermolecular forces acting on the dipeptide. The above-mentioned findings can help in developing more complex mathematical models for polypeptide folding from amino acid subunits. Key words: potential energy surface, glycyl-glycine diamide, conformational analysis, mathematical modeling. Il devient de plus en plus complexe de prévoir la façon dont se replie une protéine en trois dimensions à mesure que sa chaîne linéaire d'acides aminés s'allonge. Ainsi, en travaillant sur le problème conformationnel d'un peptide plus petit, on peut générer des idées initiales quant à la nature des principales forces moléculaires en jeu et à leur rôle dans le processus de repliement. Pour faire suite à l'étude conformationnelle des unités d'acides aminés entrant dans la composition des protéines, qui visait à permettre de comprendre la structure secondaire de peptides de petite taille, nous proposons dans le présent article des modèles mathématiques pour les nombreuses sections transversales à deux rotors de l'hypersurface d'énergie potentielle en 5D du N-acétyl-glycyl-glycine-N'-méthylamide. Nous avons extrait ces sections transversales le long de la première sous-unité de glycine, en maintenant ses coordonnées fixes aux cinq minima d'énergie du diamide de glycine. Les modèles mathématiques obtenus ont présenté un écart moyen quadratique (EMQ) de 1,36 kJ [mol.sup.-1] et un [R.sup.2] moyen de 0,9923 par rapport aux valeurs d'énergie obtenues par calculs DFT. Les géométries des minima obtenues à partir de ces modèles concordent également bien avec celles des conformères dont les minima d'énergie ont été optimisés par DFT. Un aspect important de cette étude touche également la relation entre la surface d'énergie potentielle (SEP) du diamide de glycyl-glycine et celle de ses sous-unités de glycine. Dans la première sous-unité de glycine, nous avons observé des écarts pouvant atteindre 28,35 kJ [mol.sup.-1] et 29,52 kJ [mol.sup.-1] entre les sections transversales de la SEP le long des conformations [[gamma].sub.L] et [[gamma].sub.D], respectivement. Ces résultats permettent de penser que des forces intermoléculaires squelette-squelette importantes agissent sur le dipeptide. Les observations précitées peuvent servir à mettre au point des modèles mathématiques plus complexes pour prédire le repliement de polypeptides à partir de leurs sous-unités d'acides aminés. [Traduit par la Rédaction] Mots-clés : surface d'énergie potentielle, diamide de glycyl-glycine, analyse conformationnelle, modélisation mathématique., Introduction The protein folding problem, which is the process of how a linear sequence of amino acids acquires its biologically active three-dimensional shape, is still an open problem in molecular [...]

Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and intermolecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ [mol.sup.-1], which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations. Key words: potential energy surface, conformational analysis, mathematical modeling. La prediction de la structure tridimensionnelle d'une proteine a partir de sa sequence d'acides amines requiert une parfaite comprehension des forces moleculaires qui influencent le processus de repliement des proteines. Chacune des conformations possibles possede sa propre energie potentielle, laquelle caracterise sa stabilite thermodynamique. Ces connaissances sont necessaires pour la determination des interactions primaires intra et intermoleculaires, de maniere a pouvoir reduire la dimensionnalite du probleme et creer une representation relativement simple du systeme. L'etude de ce probleme a l'aide de methodes de chimie quantique, bien que produisant des resultats exacts, necessite aussi des ressources informatiques considerables. Dans le cadre de la presente etude, nous proposons une fonction d'energie potentielle a deux rotors pour representer les interactions du squelette d'acides amines, par une combinaison lineaire d'une serie de Fourrier et d'un amalgame de fonctions gaussiennes. Nous avons applique cette fonction a l'approximation des surfaces d'energie potentielle (SEP) de type Ramachandran des 20 acides amines d'un diamide. Les resultats ont produit un ecart moyen quadratique de 2,38 kJ*[mol.sup.-1], ce qui laisse supposer que ce modele mathematique represente bien la topologie generale de sa surface d'energie potentielle conformationnelle. De plus, cet article fournit des informations sur les conformations preferentielles de diamides d'acides amines grace a la geometrie des minima locaux et aux intervalles energetiques obtenus au moyen de ce modele mathematique ameliore. Le modele mathematique que nous pro-posons offre une representation simplifiee en vue d'etablir un cadre pour la construction de modeles de polypeptides a partir des fonctions des acides amines qui le composent et, par consequent, constitue une nouvelle methode pour l'evaluation rapide et exacte des energies potentielles aux fins de modelisation de biomolecules. [Traduit par la Redaction] Mots-cles : surface d'energie potentielle, analyse conformationnelle, modelisation mathematique., Introduction Proteins, which are assembled from 20 amino acids, are machines and building blocks of living cells. The macromolecules are vital for structure, function, and regulation of various biological processes. [...]

Abstract: The conformational potential energy surface (PES) of a molecule provides insights into the relative stability of the possible foldamers. However, the time and space complexity of electronic structure calculations, [...]

Both the gas phase and solid phase environmental pollution produce double problems. The first is to reduce the current pollutants and the second is to stop producing further pollutants. The first is the simpler because existing technologies are satisfactory although expensive. The second problem is more involved because new technologies need to be developed. Such developments are not only expensive, but require decades of major scientific and engineering efforts. This paper focuses only on the second, the more difficult problem. [ABSTRACT FROM AUTHOR]

Noradrenaline is a neurotransmitter that is involved in various psychological processes. In the neurotransmission process, noradrenaline binds to an adrenergic receptor by forming a complex of hydrogen bonds between its two catechol ring hydroxyl groups and the amino acid residues of adrenergic receptors. Although the two catechol ring hydroxyl groups play a crucial role in making hydrogen bonds to the binding site of the adrenergic receptor, the contribution of the catechol ring hydroxyl groups to the intramolecular stability that may affect docking has not been fully studied. To reveal the specific role that the catechol ring hydroxyl groups might play in stabilizing noradrenaline, the quantum chemical computations of geometry optimization and thermodynamic functions of N-protonated noradrenaline conformers were performed at both the B3LYP/6-31G(d,p) and G3MP2B3 levels of theory, using the Gaussian 03 program. The results were compared with those of N-protonated β-hydroxy-β-phenylethylamine, which is identical to noradrenaline except it lacks two catechol ring hydroxyl groups. For the first time, post-Hartree-Fock computations were used to obtain thermodynamic functions to establish relative stabilities of all possible conformers of N-protonated noradrenaline. In this study, 18 distinct structures of N-protonated noradrenaline were revealed, and the catechol ring hydroxyl groups were found to affect noradrenaline stability positively or negatively depending on the conformational orientations. On the basis of available experimental results, the issue that the least stable conformation of two catechol ring hydroxyl groups may be involved in the docking process has been raised. These findings may be useful in synthesis of derivatives of noradrenaline in drug design. Key words: noradrenaline, density functional calculations, thermodynamic functions, conformational stability, intramolecular hydrogen bond. La noradrenaline est un neurotransmetteur implique dans divers processus psychologiques. Dans le processus de neurotransmission, la noradrenaline se lie a un recepteur adrenergique par formation d'un complexe de liaisons hydrogenes entre les deux groupes hydroxyles de son noyau catechol et les residus d'acides amines des recepteurs adrenergiques. Meme si les groupes hydroxyles de son noyau catechol jouent un role important dans la formation des liaisons hydrogenes avec le site de fixation du recepteur adrenergique, la contribution des groupes hydroxyles de son noyau catechol a la stabilite intramoleculaire qui peut affecter l' arrimage n' a pas ete completement etudie. Afin d' evaluer le role specifique que les groupes hydroxyles de son noyau catechol peuvent jouer dans la stabilisation de la noradrenaline, on a effectue des calculs de chimie quantique d'optimisation de la geometrie et des fonctions thermodynamiques des conformeres de la noradrenaline N-protonee, en faisant appel au programme << Gaussian 03 >>, aux niveaux B3LYP/6-31G(d,p) et G3MP2B3 de la theorie. Les resultats ont ete compares a ceux obtenus avec la β-hydroxy-β-phenylethylamine N-protonee, qui est identique a la noradrenaline al' exception de l' absence des deux groupes hydroxyles du noyau catechol. Des calculs post-Hartree-Fock ont donc ete utilises pour la premiere fois pour obtenir des fonctions thermodynamiques dans le but d' etablir les stabilites relatives de tous les conformeres possibles de la noradrenaline N-protonee. Dans cette etude, on a mis en evidence 18 structures distinctes de la noradrenaline N-protonee et on a trouve que les groupes hydroxyles du noyau catechol affectent la stabilite de la noradrenaline positivement ou negativement suivant les orientations conformationnelles. Sur la base des resultats experimentaux disponibles, il a ete suggere que la conformation la moins stable des deux groupes hydroxyles du noyau catechol pourrait etre impliquee dans le processus d'arrimage. Ces observations pourraient s'averer utiles dans la planification de la synthese de derives de la noradrenaline. Mots-cles : noradrenaline, calculs de la fonctionnelle de la densite, fonctions thermodynamiques, stabilite conformationnelle, liaison hydrogene intramoleculaire. [Traduit par la Redaction], Introduction A number of neurotransmitter systems, including noradrenaline, serotonin, and dopamine, are closely linked with various psychological processes, including mood regulation. Specifically, the dysfunction within noradrenaline system may lead to [...]

Stabilities and conformational properties of two Pro related to Thr point mutation models are computed at the B3LYP/6-31 G(d) level of theory for the parent triamino acid diamide Pro-Pro-Pro (HCO-Pro-Pro-Pro-N[H.sub.2]). Study describes an approach to analyzing a point mutation at the center of a peptide chain.

The omega-3 polyunsaturated fatty acids (PUFA) like stearidonic acid (SDA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and its chain fragment models are studied and significant conformations are selected for the cis and trans isomers to obtain the thermodynamic functions for the cis-trans isomerization and for folding. The structural analysis has shown some significant differences in thermodynamic function of the trans- and cis-PUFAs.

Structural investigations of a set of model beta-peptides were performed at different levels of theory in order to characterize the sheet assembly properties of beta-peptides. It was found that sheets of beta-peptides have fundamentally different behaviors when compared to alpha-peptides.

The conformational process within one of the simplest molecules, n-butane, is computed as a function of rotation around the central C-C bond. The conformational entropy function calculated from 3N - 7 internal degrees of freedom was found to be a continuous function of rotational folding.

Computational and experimental determinations are carried out in parallel on the conformational probability of N-Acetyl-Phenylalanine-NH2. Experimental and theoretical carbonyl stretches are compared and showed good agreement adding further strength to the synergy between experiment and theory.

The activation parameters of the pericyclic Meisenheimer rearrangement and a competitive rearrangement of N-propargylmorpholine N-oxide are determined by experimental and computational methods. A number of aprotic and protic solvents of different polarities and hydrogen bond-forming abilities and the roles of electron-pair acceptor additives are investigated.

The development of the carvedilol molecule methodology, consisting of three fragments, investigated earlier, are used to predict and optimize a comprehensive list of possible carvedilol conformations, based on low-energy fragment conformations, to determine the conformations of carvelilol that are expected to dominate a gas-phase sample. The results revealed that using a rational molecular fragmentation method, nine converged low-energy conformations were discovered, seven of which possessed a unique tetra-centric conformational motif not previously determined.

The hydrogen bonds involving the methyl group were studied by topological analysis of the electron density derived from quantum mechanical geometry-optimized structures of selected molecules/ions. The results indicated that hydrogen-bond formation not only depends on the distance from the methyl group to the proton acceptor X but also on the angle CH.X.