Relazione tra traffico nautico e tursiopi (Tursiops truncatus) nell’Isola di Lampedusa (Stretto di Sicilia, Mar Mediterraneo).

Ab initio study on the photoisomers of a nitro-substituted spiropyran

Structural and spectroscopic properties of the photoisomers of a nitro-substituted spiropyran have been investigated by performing ab initio molecular orbital (MO) calculations both in vacuo and in hexafluoro-2-propanol solution. Full geometry optimisation of the closed form and of the transoid conformations of the open form has been carried out. Dipole moments of both photoisomers have been determined, the ratio of which agrees with recent experimental results. Net atomic charges have also been determined according to three different approaches.

Density Functional Theory Study of the Trans-Trans-Cis (TTC)→Trans-Trans-Trans (TTT) Isomerization of a Photochromic Spiropyran Merocyanine

Density Functional Theory (DFT) calculations have been performed on the TTC→TTT isomerization reaction of the open forms of the 1',3'-dihydro-8-bromo-6-nitro- 1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-(2H)indole (8-Br-6-nitro-BIPS) system. The calculations were carried out in vacuo and in methylene chloride solution at different temperatures. Results are compared with the available experimental values of free energy difference and activation energy in solution.

X‐ray Absorption Spectra of Cu II and Cu III Complexes of N , N ′ ‐1,2‐Phenylenebis(2‐mercapto‐2‐methylpropionamide)

The X-ray absorption spectra of Cu I I and Cult complexes of N,N'-1,2-phenylenebis(2-mercapto-2-methylpropionamide) were recorded and analysed in solid phase. The EXAFS spectra of the two samples were refined with full multiple scattering path. Geometry optimisations on the Cu I I and Cu I I I complexes were performed by the B3LYP density functional method, with the 6-31G(d,p) basis set, considering different spin multiplicities. The singlet state of the Cu I I I complex was shown to be more stable than the triplet state, and a good agreement between the calculated and the corresponding experimental structure was found. Further single-point calculations on the optimised geometry were carrie…

Simulazione del trasporto dello ione Na+ attraverso un aggregato tubolare ciclopeptidico

DFT computational study on Fe(III)-N,N′-ethylene-bis(salicylideneiminato) derivatives

DFT calculations, at unrestricted B3LYP level, have been performed on the structures of three iron(III) complexes, Fe(Salen)Cl, [Fe(Salen)]+ and [Fe(Salen)OH2]+, where Salen is the anion of Schiff base ligand N,N′-ethylene-bis (salicylideneimine), considering the spin multiplicity (S) values 2, 4 and 6. The results obtained have been compared with the available structural an magnetic experimental data, allowing us to conclude that a stable form of the FeIII(Salen) complex in aqueous solution should be characterized by an energy stabilization of the S=4 compared to the S=6 state.

Theoretical calculation of the vibrational spectra of cis-cis-cyclooctadienes in the vapour phase.

The theoretical infrared spectra of 1,3-cis-cis-cyclooctadiene (1,3-COD) and 1,5-cis-cis-cyclooctadiene (1,5-COD), were obtained by ab initio MO calculations at Hartree-Fock level. The results were compared with the available IR experimental spectra of 1,3- and 1,5-COD. The apparent agreement between theoretical and experimental data allows us to exploit two bands, found only in the case of the theoretical spectrum of 1,4-COD, as a tool for identifying 1,4-COD during its synthesis.

Hydrogenation of acetylene-ethylene mixtures on Pd catalysts: study of the surface mechanism by computational approaches. Metal dispersion and catalytic activity

The hydrogenation mechanism of acetylene–ethylene mixtures on Pd catalysts under different experimental conditions was studied by employing a time-dependent Monte Carlo approach set to use a fixed series of event probabilities. The dependence of the catalyst activity and selectivity on the sizes of the metal particles was simulated at microscopic level and the results, also refined by fitting procedures, suggested proper explanations for the apparent nonuniformity of the related experimental findings. The use of the steric hindrance parameter of the surface species and the available surface energy on the metallic catalyst sites was decisive for reproducing the experimental results.

Conformational analysis of methyl-substituted 9,10-dihydroanthracenes

The amount of the ring puckering in methyl-substituted 9,10- dihydroanthracene was theoretically determined through DFT calculations. Theoretical calculations allowed to obtain the geometrical structures and energetic data on the different considered isomers.

Semiempirical calculations on the interaction between dimethyltin(IV) and DNA model system

Abstract The interaction between a dinucleotide triphosphate duplex (DD), mimicking the DNA molecule, and the dimethyltin(IV) cation is studied by the semiempirical PM3 method. The results show that the interaction can occur involving the tin atom and the electron-donor centres of DD, requiring in some cases the presence of water molecules. In particular, the binding of the dimethyltin(IV) moiety with two adjacent phosphate oxygen atoms is allowed by the presence of water molecules coordinating to the tin atom. In this case the tin environment shows a geometry in agreement with 119 Sn Mossbauer and X-ray data.

Theoretical study of the interaction between an organic tubular structure and the Na+ ion

A new algorithm to explain adsorption-desorption processes on metal surfaces

Conformational analysis of N-hydroxyurea in the gas phase

Hydrogen on palladium clusters: a quantum chemical study

Structural and spectroscopic study of the Br2...3-Br-pyridine complex by DFT calculations.

Abstract The structure and the Raman vibrational spectrum of the complex Br 2 ⋯3-Br-pyridine are determined by DFT calculations using different parametrizations. The calculations are performed taking into account the effects of the dichloromethane as solvent by the CPCM method. A value of 39 kJ mol −1 for the formation enthalpy and of 1 kJ mol −1 for the formation free energy at room temperature in presence of the solvent is found. The predicted Raman spectrum is compared with the experimental one and the essential features of the spectrum are well reproduced by the B3LYP parametrization. The intensity changes of the bands when going from the free moieties to the complex are also generally …

Catalytic activity of T22 H-ZSM-5 zeolite on the trans–cis 2-butene isomerization

Dynamics of Metal Centers Monitored by Nuclear Inelastic Scattering

Nuclear inelastic scattering of synchrotron radiation has been used now since 10 years as a tool for vibrational spectroscopy. This method has turned out especially useful in case of large molecules that contain a M\"ossbauer active metal center. Recent applications to iron-sulfur proteins, to iron(II) spin crossover complexes and to tin-DNA complexes are discussed. Special emphasis is given to the combination of nuclear inelastic scattering and density functional calculations.

DFT calculations of the electric field gradient of tin compounds: a structure elucidation tool by 119Sn Mossbauer spectroscopy.

Theoretical evaluation of structures and energetics involved in the hydrogenation of hydrocarbons on palladium surfaces

Abstract Quantum mechanical calculations were employed to deepen information about the basic properties of the mechanism occurring in the palladium catalytic hydrogenation involving surface hydrogen species of unsaturated hydrocarbons. Activation energy values of elementary events implicated in the whole reaction were computed by potential energy surface analyses, to determine the corresponding occurrence probabilities of the same events. Different surface hydrogen species were pointed out and their relevance in the overall surface process was discussed together with their geometrical and chemical characteristics.

Ab initio study of the tautomeric forms of some quinolinediones

Abstract 7,8-dihydroquinoline-4,5 (1 H ,6 H )-dione ( 1 ) and 7,8-dihydroquinoline-2,5-(1 H ,6 H )-dione ( 2 ) in their tautomeric oxo and hydroxy forms have been studied by ab initio Hartree-Fock calculations; tautomerization energies predict a more stable hydroxy structure having an intramolecular hydrogen bond for compound 1, whereas the oxo form is slightly-preferred for compound 2. Fourier Transform-Infra Red (FT-IR) spectra in CHCl 3 solution indicate that the predicted most stable tautomers in the vapour phase remain as such.

X-ray absorption spectra of Cu(II)- and Cu(III)- complexes of N,N’-1,2-phenylenebis(2-mercapto-2-methyl-propionamide)

Ab initio conformational study of 2,2′:5′,2″-terthiophene

Abstract The conformers of 2,2′:5′,2″-terthiophene were determined through ab initio MO full geometry optimization with a 6-31G * basis set. Different minima were found corresponding to twisted anti, anti, syn, anti and syn, syn structures. An estimate of the interconversion rate between conformers was performed.

Theoretical study of degenerate Boulton-Katritzky rearrangements. Semiempirical and ab initio procedures

Abstract A theoretical study of degenerate Boulton–Katritzky rearrangements concerning the anions of the 3-formylamino-1,2,4-oxadiazole, 3-formylmethyl-isoxazole and 3-hydroxy-iminomethyl-1,2,5-oxadiazole has been carried out by using semiempirical MNDO and ab initio Hartree–Fock procedures. Different transition structures and reactive pathways were obtained in the two cases. Semiempirical treatment shows asymmetrical transition states and non-concerted processes via symmetrical intermediates. By contrast, ab initio procedures describe concerted and synchronous processes involving symmetrically-located transition states. Some comments and criticisms on the theoretical treatment of these typ…

Structural and spectroscopic characterisation of 2-(2'-hydroxybenzoyl)pyrrole and its O-methyl derivative

Abstract Density functional theory calculations on the tautomeric and conformational equilibria of 2-(2′-hydroxybenzoyl)pyrrole (HBP) and 2-(2′-methoxybenzoyl)pyrrole (MBP) were performed. Moreover, the experimental IR and UV spectra of the same compounds were recorded and compared with the theoretical data. The presence of an intramolecular hydrogen bond in HBP can be related to the biological activities of some of its derivatives.

The electronic spectra of 2-(2′-hydroxybenzoyl)pyrrole and 2-(2′-methoxybenzoyl)pyrrole: a theoretical study

The gas-phase electronic spectra of 2-(2 0 -hydroxybenzoyl)pyrrole and 2-(2 0 -methoxybenzoyl)pyrrole have been determined using multiconfigurational perturbation theory (CASPT2). Solvatochromic spectral shifts for these molecules have been measured in cyclohexane and methanol and the electrostatic components of these shifts have been estimated using the vertical electrostatic model (VEM 4.2) developed for the configuration interaction with single excitations model implemented with the intermediate neglect of differential overlap Hamiltonian (CIS/INDO/ S2). Comparison between theory and experiment and an interpretation of the main spectral differences between the two substituted pyrroles an…

Studio teorico della reazione di idroisomerizzazione del cis-butene su cluster di palladio supportato

Theoretical study of the interaction between sodium ion and a cyclopeptidic tubular structure.

DFT calculations have been carried out to describe the pathway of a sodium ion along the stacking direction of a tubular structure set up by five cyclopeptidic units, which can be considered a suitable model of a hollow tubular structure of indefinite length. A lattice of points inside the tubular structure is defined and the DFT interaction energy values with a sodium ion are obtained. The data allow predicting a zigzag path of the ion inside the hosting structure. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007

DFT Calculations of the Electric Field Gradient at the Tin Nucleus as a Support of Structural Interpretation by119Sn Mössbauer Spectroscopy

DFT calculations, using an all-electron basis set and with full geometry optimization, were performed on 34 Sn(II) and Sn(IV) compounds of known structure and (119)Sn Mössbauer parameters, to obtain the theoretical values of the electric field gradient components, V(xx), V(yy), and V(zz), at the tin nucleus. These were used to determine the quantity V = V(zz)[1+ 1/3((V(xx) - V(yy))/((V(zz))(2)](1/2), for each investigated compound, which is related to the quadrupole splitting (DeltaE) parameter according to DeltaE = 1/2eQV, where e is the electronic charge and Q is the quadrupole moment of the tin nucleus. The linear fitting of the correlation plot of the experimental DeltaE, versus the cor…

A new suggested class of organic tubular structures

A DFT study has been performed on monomers and dimers of new cyclic structures, cyclodioxabislactams, which are expected to bring about tubular structures through a stacking process settled by hydrogen-bonding between antiparallel peptidic groups. Different stacking modes have been found with significant effects on the energetics of the assembling process.

ONIOM study on the equilibrium geometries of some cyclopeptides

Abstract The geometries of two octacyclopeptides, cyclo[( d -AmP- l -AmP) 4 ] (AmP=α-aminopentanoic acid) and cyclo[( d -Ala- l -Phe) 4 ] were obtained by DFT and ONIOM methods. The resulting data show a substantial agreement with a computing time about three times lower in the case of the ONIOM procedure. This can be exploited in the study of polymeric structures set up by cyclopeptidic monomeric units.

Ab initio calculations on the molecular structure of fluorocyanopolyynes

Abstract The molecular structure of the first three members of the fluorocyanopolyynes was studied by ab initio Hartree-Fock calculations with a polarized double zeta basis set and at MP2 level with the same basis set. Alternating triple and single bonds were found; a theoretical estimate of rotational constants and dipole moments was performed and a comparison with the available experimental data was made. An analysis of the theoretical vibrational frequencies of the title compounds was carried out.

DFT studies on catalytic properties of isolated and carbon nanotube supported Pd9 cluster. Part II. Hydro-isomerization of butene isomers

The processes involved in the butene hydro-isomerization, occurring on a small palladium cluster in the presence of dissociated hydrogen, have been investigated by means of DFT and DFT/MM approaches. This study has been performed both on an isolated (unsupported) Pd(9) cluster and on the same cluster when it is supported on a portion of a single-walled armchair(6,6) carbon nanotube. The study follows another investigation which has already been published concerning the adsorption, fragmentation and diffusion of hydrogen on the same metal cluster. The main aspects involved in the parallel reaction steps of the whole hydro-isomerization mechanisms are not strongly affected by the presence of …

CASSCF/CASPT2 analysis of the fragmentation of H2 on a Pd4 cluster

Two reactive pathways are described for the dissociative adsorption of a hydrogen molecule on a Pd4 pyramidal cluster, by using DFT/B3LYP and CASSCF/CASPT2 computational methods. Because of the different spin multiplicities of the cluster in the initial and final states, the reaction proceeds through a spin multiplicity change, which occurs close to the transition states. The activation energy values are very similar when the DFT method is used, whereas the CASPT2 calculations predict that the concerted mechanism is disfavored. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Studio teorico sul confinamento delle azidi di metalli alcalino-terrosi nella cavità di un aggregato tubolare ciclopeptidico

Adsorption and reaction of small molecules on palladium clusters: DFT studies

Computational Study on Cesium Azide Trapped in a Cyclopeptidic Tubular Structure

The structures and the electronic properties of host-guest complexes formed by a cyclopeptidic tubular aggregate and the species CsN3, CS2(N-3)(2), and CS2N6 have been investigated by means of density functional theory. Taking advantage of the azide property to act as a bridge ligand between two or more metal cations, it may be possible to trap N-3(-) ions inside a confined space. This could be important for the preparation of polynitrogen molecules N-n. Results show that there are significant attractive interactions between the azide ion and the cavity walls, which make the ion stay inside the inner empty space of the cyclopeptidic aggregate. The confinement of the species CS2(N-3)(2) forc…

Ab initio calculations and vibrational spectroscopy on the phenylenediamine isomers

Molecular orbital calculations at HF and MP2 levels have been performed using the 6-3IG** basis set for full geometry optimization of the phenylenediamine isomers. Our results show that only a transoid conformer is found for o-phenylenediamine, whereas cis and trans conformers exist for m- and p-phenylenediamine. Vibrational normal modes have been also analyzed for the gas phase and in chloroform solution, and compared with experimental data we have obtained using FTIR spectroscopy. © 1998 Elsevier Science B.V.

DFT studies on catalytic properties of isolated and carbon nanotube supported Pd9 cluster–I: adsorption, fragmentation and diffusion of hydrogen

The processes of adsorption, fragmentation and diffusion of hydrogen on a small palladium cluster have been investigated by means of DFT and DFT/MM approaches. These studies have been performed by considering a D(3h) symmetry Pd(9) in the isolated state as well as when supported on a portion of single-walled armchair(6,6) carbon nanotube. The hydrogen fragmentation process easily occurs on the bare Pd(9) cluster, involving energy barriers of 25-35 kJ mol(-1) and the drop in spin multiplicity on passing from the reactant to the product. The atomic hydrogen diffuses through the cluster atoms with energy barriers, which do not exceed 20 kJ mol(-1), with some positions clearly identifiable as t…

Computational study of dimethyl- and trimethyl-tin(IV) complexes of porphyrin derivatives

The molecular geometry, energetics and electronic charge distribution of diorgano- and triorgano-tin(IV) complexes of [protoporphyrin-IX] and [meso-tetra(4-carboxyphenyl)porphine] derivatives were determined at semi-empirical and ab initio levels. To study the molecular details of the complexes, simpler molecule models were calculated by the ab initio pseudo-potential method. The molecular properties of these complexes are essentially independent of the presence of the peripheral tin atoms. Agreement was always found among the results of the different computational approaches, as well as between the theoretical and the experimental findings on the molecular geometry of the hypothesized comp…

DFT study of reduction reactions on a palladium cluster supported on a carbon nanotube

Semi-empirical MNDO study of the structure of some diorganotin (IV) glycylglycinates

The geometrical structures of some diorganotin glycylglycinates have been obtained using the MNDO semi-empirical method. A good agreement with the experimental diffractometric data was found.

Tin-DNA complexes investigated by nuclear inelastic scattering and synchrotron radiation

Theoretical study of spiropyran-merocyanine thermal isomerization.

Abstract Quantum mechanical computations at DFT level were carried out on the processes involved in the thermal reaction SP ⇆ ME, where SP is the nitro-substituted spirobenzopyran (1 ′ ,3 ′ -dihydro-1 ′ ,3 ′ ,3 ′ -trimethyl-6-nitro-spiro[2H-1-benzopyran-2,2 ′ - [2H]indole]) in the closed form and ME is the corresponding open form. A detailed theoretical description of the overall reaction is reported along with the thermodynamic parameters for all intermediates and transition states. The obtained activation energy value is in agreement with the available experimental data in solution.

The molecular structure of N-hydroxyurea

Ab initio calculations were performed on the tautomers and conformers of N-hydroxyurea using a 6-31G** basis set. The minimum-energy structures have been found and the importance of the intramolecular hydrogen bond as the stabilizing factor was pointed out. © 1996 John Wiley & Sons, Inc.

Theoretical designing of new organic tubular structures

CASSCF/CASPT2 analysis of the fragmentation of H2 on a Pd4 cluster

Two reactive pathways are described for the dissociative adsorption of a hydrogen molecule on a Pd4 pyramidal cluster, by using DFT/B3LYP and CASSCF/CASPT2 computational methods. Because of the different spin multiplicities of the cluster in the initial and final states, the reaction proceeds through a spin multiplicity change, which occurs close to the transition states. The activation energy values are very similar when the DFT method is used, whereas the CASPT2 calculations predict that the concerted mechanism is disfavored.

Studio teorico dell’interazione host-guest fra un sistema tubolare ciclopeptidico e la cesio azide

An ab initio study of the tautomeric equilibria of the N-oxides of hydroxypyridines in the vapour phase

Abstract An ab initio self-consistent field molecular orbital study of the N-oxides of hydroxypyridines has been carried out. The optimized structures have been obtained at the 6-31G ∗ level, and the energy values have been computed at the 6-31G ∗ and MP2-6-31G ∗ //6-31G ∗ levels. The tautomerization energies for the three couples of systems in the vapour phase have been evaluated.

Montecarlo calculation of the structure of liquid acetonitrile

Abstract A Montecarlo calculation of the structure of liquid acetonitrile, based on a Lonnard-Jones ab initio potential, has been performed. Pair correlation functions between all the heavy atoms are obtained for distances within 8 A°. The features of the obtained structure are discussed.

Theoretical study of a palladium cluster on carbonaceous supports

Theoretical study of the insertion of sodium ion into organic tubular structures

Theoretical Study of Palladium Cluster Structures on Carbonaceous Supports

DFT calculations have been performed on a palladium cluster adsorbed on two different carbonaceous supports, namely, two stacked polycircumcoronene units mimicking a double layer of graphite and a portion of an armchair (6,6) carbon nanotube. All of the systems have been subjected to geometry optimization and electronic structure investigation. This work, which is part of an extensive computational study on heterogeneous catalytic systems, is devoted to identify electronic and geometrical changes in which metal clusters and supports are involved upon interaction. Such analysis is helpful in designing new heterogeneous metallic catalysts, namely, new metal-supported carbonaceous catalysts. C…

N -Diphenylmethyl-2-propenamide: theoretical study of the structure and interaction with a DNA model system

Abstract N -diphenylmethyl-2-propenamide (NDP) was synthesised and characterised. Pharmacological in vitro tests pointed out that NDP had a cytotoxic activity on a human ovarian carcinoma comparable to that of doxorubicin. Hypothesising that this in vitro cytotoxic activity could be mainly due to intercalating interactions, between the drug and DNA fragments, ab initio calculations, at the Hartree–Fock (HF) level, were performed on the structure, and on the conformational properties of NDP, whereas its interaction with an (AC)(TG) dinucleotide triphosphate duplex (DD) was studied by the ONIOM method, at HF and PM3 level for NDP and DD, respectively. The supposed intercalation process with t…

The interaction of deoxyribonucleic acid with methyltin(IV) moieties in solution studied by small-angle X-ray scattering, circular dichroism and UV spectroscopy

The nature of calf thymus DNA in aqueous solution, in the presence of the organotin(IV) species Sn IV Me 3 , Sn IV Me 2 and Sn IV Me, possibly partly hydrolysed and/or hydrated, was investigated by small-angle X-ray scattering (SAXS), ultraviolet spectroscopy (UV) at different temperatures and circular dichroism (CD). The results are compared with those of previous 119 Sn Mossbauer studies on condensed DNA phases. The effects of tin-phosphate oxygen bonding on the DNA melting profile in DNA-Sn IV Me systems are in agreement with previous reports on DNA-Main Group metal ion interactions. The structure and conformation of the DNA double helix are not influenced by Sn IV Me n species, even in …

Ab initio study of lithiated N-methylpyridones