Free energies of adsorption of amino acids, short linear peptides and 2,5-piperazinediones on silica from water as estimated from high-performance liquid-chromatographic retention data

Equilibrium constants (K) and free energies (— G) of adsorption of amino acids, short linear peptides and cyclic dipeptides (2,5-piperazinediones) on silica from neutral aqueous solutions were calculated from the retention values measured by means of high-performance liquid chromatography on a silica gel column. For most amino acids and linear peptides — G values were negative and K < 1, thus showing very weak adsorption. 2,5-Piperazinediones exhibited higher adsorbability (for most of them, — G > 0 and K > 1) as compared to related dipeptides. Influence of the structure of a-substituent on the adsorbability is analyzed. A linear dependence of — G on the number of aliphatic carbon atoms in a sorbate molecule was found for the series of aliphatic bifunctional amino acids, related dipeptides and 2,5-piperazinediones, as well as for the group from glycine to triglycyl glycine.     

PM3, AM1, MINDO3 semi-empirical IR spectra simulations for some nitriles of interest for Titan's chemistry

A set of the semi-empirical methods (PM3, AM1, MNDO and MINDO3) has been tested to find the best auxiliary tool for the identification of nitriles by gas chromatography/Fourier transform IR spectroscopy/mass spectrometry, considering five nitriles of interest for Titan's chemistry as test compounds: acetonitrile, acrylonitrile, cyanoacetylene, 2-butynenitrile and dicyanoacetylene. Of the four semi-empirical methods, MNDO can be considered as the most advantageous auxiliary tool for the gas chromatography/Fourier transform IR spectroscopy/mass spectrometry (GC/FTIR/MS) identification of nitriles of interest for Titan's atmospheric chemistry, since (1) the simulated IR spectra best match the experimental (in some cases AM1 gives comparable results); (2) it provides the best linearity between the calculated and experimental frequencies (correlation coefficient of 0.990); a scaling factor of 0.90 can be applied to afford better correspondence between the calculated and experimental wavenumbers. At the same time, none of the methods is able to predict infrared intensities and a spectral intensity pattern.     

Formation of interstellar vinyl alcohol via simple radical processes: Theoretical study

Density functional theory calculations at the B3LYP/6‐31++G(d,p) level of theory were employed to verify whether the formation of vinyl alcohol (VA) in the interstellar medium can be explained by reactions of common and abundant interstellar species such as acetylene, radicals C₂, HC? C · , · OH, and H · . Several reaction sequences are possible. They include radical combinations, which proceed without activation barriers and are highly exothermic. The reactions of closed‐shell species acetylene and HC?C‐OH with hydrogen atoms, as well as H‐transfer and OH‐rotation processes, might require activation energy. Nevertheless, either the corresponding transition states lay below the reactant level or there are alternative routes that involve no transition states at all, such as the reaction sequences C₂ → HC?C · → HC?CH → trans‐syn‐HC( · )?CH‐OH → syn‐VA; C₂ → HC?C · → syn‐?C?CH‐OH → (trans or cis)‐syn‐HC( · )?CH‐OH → syn‐VA; and C₂ → · C?C‐OH → syn‐:C?CH‐OH → (trans or cis)‐syn‐HC( · )?CH‐OH → syn‐VA. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Deposition of gold nanoparticles onto thiol-functionalized multiwalled carbon nanotubes

Gold nanoparticles were deposited on the surface of multiwalled carbon nanotubes (MWNTs) functionalized with aliphatic bifunctional thiols (1,4-butanedithiol, 1,6-hexanedithiol, 1,8-octanedithiol, and 2-aminoethanethiol) through a direct solvent-free procedure. Small gold particles, with a narrow particle size distribution around 1.7 nm, were obtained on 1,6-hexanedithiol-functionalized MWNTs. For MWNTs functionalized with the aminothiol, the average Au particle size was larger, 5.5 nm, apparently due to a coalescence phenomenon. Gatan image filter (GIF) observations show that sulfur is at the nanotube surface with a non-homogeneous distribution. A higher sulfur concentration was observed around the gold nanoparticles' location.     

Interaction of porphine and its metal complexes with C60 fullerene: a DFT study

We performed DFT calculations (BLYP general-gradient approximation in conjunction with a double numerical basis set) for the interaction of free porphine ligand and a number of its metal complexes with C60 molecule to analyze how the nature of a central metal ion influences the geometry and electronic characteristics (electrostatic potential and spin density distribution and highest-occupied molecular orbital (HOMO) and lowest-unoccupied molecular orbital (LUMO) structure). We found that the presence of a central metal ion is crucial for a strong interaction. The energy of interaction between H2P and C60 is -0.3 kcal mol(-1) only, whereas the formation energies for the metal complexes vary from -27.3 kcal mol(-1) for MnClP.C60 to -45.8 kcal mol(-1) for MnP.C60. As a rule, the formation energy correlates with the separations between porphinate and fullerene molecules; the Mn and Fe complexes exhibit the closest approach of ca. 2.2 A between the metal ion and carbon atoms of C60. In most porphine-C60 complexes studied, the two closest contacts of central metal ion or H are those with carbon atoms of the (6,6) bond; VOP.C60 is the only exception, where the closest V...C contacts involve the (5,6) bond. The macrocycle geometry changes, and the magnitude of the effect depends on the central atom, being especially dramatic for Mn, MnCl, and Fe complexes. The shape of LUMOs in most complexes with C60 is not affected notably as compared to the LUMO of the isolated C60 molecule. In the case of Fe, the HOMO extends from the central atom to two opposite pyrrol rings. At the same time, the HOMO-LUMO gap energy decreases drastically in most cases, by ca. 20-30 kcal mol(-1). For electrostatic potential distribution, we systematically observed that the negative lobe contacting C60 shrinks, whereas the opposite one becomes notably bigger. In the case of paramagnetic complexes of VO, Mn, FeCl, Co, and Cu, spin density distribution was analyzed as well.     

[80]Fullerene–amino acid interactions: Theoretical insights

This work reports the interactions of a C₈₀ fullerene species with the 20 naturally occurring amino acids. As a result of the analysis of multiple configurations, we have determined that the most stable C₈₀ complexes form with thiol containing amino acids. The stabilities of the resulting complexes have been classified according to biochemical classifications that are used to develop trends among the calculated data. The computed trends in the dissociation energies are related to the backbone structure of the corresponding amino acids. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

PM3, AM1, MNDO and MINDO3 semi-empirical IR spectra simulations for compounds of interest for Titan's chemistry: diazomethane, methyl azide, methyl isocyanide, diacetylene and triacetylene

Four semi-empirical methods (PM3, AM1, MNDO and MINDO3) have been tested to find the best auxiliary tool for the gas chromatography/Fourier transform IR spectroscopy/mass spectrometry (GC/FTIR/MS) identification of five compounds of interest for Titan's atmospheric chemistry as test compounds: diacetylene, triacetylene, diazomethane, methyl azide, methyl isocyanide. Of the four methods, MINDO3 can be considered as the most appropriate method to facilitate the identification of such and similar compounds, since (1) the simulated IR spectra best match the experimental spectra for four compounds of five studied; and (2) MINDO3 provides the best linearity between the calculated and experimental frequencies (correlation coefficient of 0.995; a scaling factor of 0.84 can be applied to afford better correspondence between the calculated and experimental wavenumbers). None of the semi-empirical methods tested is able to predict (even approximately) infrared band intensities, and therefore a spectral intensity pattern.     

(C‐rac‐5,5,7,12,12,14‐Hexamethyl‐1,4,8,11‐tetraazacyclotetradecane‐κ4N)(nicotinato‐O,O′)nickel(II) perchlorate

In the title compound, [Ni(C₆H₄NO₂)(C₁₆H₃₆N₄)]ClO₄, the macrocyclic unit adopts a folded conformation, allowing the two carboxyl O atoms to occupy two neighbouring coordination sites and thus form an additional four‐membered chelate ring. The less crowded side of the macrocycle (that with the two asymmetric C—H groups) is directed towards the nicotinate anion and the asymmetric C—CH₃ groups are directed away from it. The macrocyclic NH groups neighbouring the C—CH₃ groups are also directed away from the nicotinate anion, while those NH groups which are near to the geminal methyl groups are directed towards the nicotinate anion. Although the complex does not include water mol­ecules, three types of hydrogen bond were found, involving NH groups of the macrocyclic ligand, pyridine N atoms and O atoms of the perchlorate anions.     

Spin-glass, antiferromagnetism and kondo behavior in Ce2Au1−x Co x Si3 alloys

Recently, the solid solution Ce₂Au_{1− x Co} xSi₃ has been shown to exhibit many magnetic anomalies associated with the competition between magnetic ordering and the Kondo effect. Here we report high pressure electrical resistivity of Ce₂AuSi₃, ac susceptibility (X) and magnetoresistance of various alloys of this solid solution in order to gain better knowledge of the magnetism of these alloys. High pressure resistivity behavior is consistent with the proposal that Ce₂AuSi₃ lies at the left-hand side of the maximum in Doniach’s magnetic phase diagram. The ac X data reveal that there are in fact two magnetic transitions, one at 2 K and the other at 3 K for this compound, both of which are spin-glass-like. However, as the Co concentration is increased, antiferromagnetism is stabilized for intermediate compositions before attaining non-magnetism for the Co end member.     

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

To address the choice of an appropriate value of electron smearing to facilitate self‐consistent field (SCF) convergence, we studied the interaction of doxorubicin with short armchair and zigzag single‐walled carbon nanotube models with closed caps, at the PWC/DNP level of density functional theory. By gradually reducing the electron smearing value from a large and most commonly used one of 0.005 Ha to zero (Fermi occupation), we monitored the changes in close contacts between the interacting species, total energy of the molecular system, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy and isosurfaces, HOMO‐LUMO gap energy, and plots of electrostatic potential. It became evident that the commonly used smearing values of ≥0.001 Ha can alter the results significantly (for example, by one order of magnitude for HOMO–LUMO gap energy). We suggest the setting of electron smearing value at 0.0001 Ha, which does not imply too high computation cost and can guarantee the results close to the ones obtained with Fermi occupation. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011