Structural effects and hydrogen bonds on N,N `-di(methoxycarbonylsulfenyl)urea, [CH(3)OC(O)SNH](2)CO, studied by experimental and theoretical methods

Pure N,N`-di(methoxycarbonylsulfenyl)urea, [CH(3)OC(O)SNH](2)CO, is quantitatively prepared by the hydrolysis reaction of CH(3)OC(O)SNCO and characterized by (1)H NMR, GC-MS and FTIR spectroscopy techniques. Structural and conformational properties are analyzed using a combined approach with data obtained from X-ray diffraction, vibrational spectra and theoretical calculation methods. The IR and Raman spectra for normal and deuterated species are reported. The crystal structure of [CH(3)OC(O)SNH](2)CO was determined by X-ray diffraction methods. The substance crystallizes in the orthorhombic P2(1)2(1)2 space group with a = 9.524(2), b = 12.003(1), c = 4.481 (1) angstrom, and Z = 2 moieties in the unit cell. The molecule is sited on a twofold crystallographic axis (C(2)) parallel to c and shows the anti-anti conformation (S-N single bonds antiperiplanar with respect to the opposite C-N single bonds in sulfenyl-urea-sic group). Neighboring molecules are arranged in a chain motif that extends along the C(2)-axis and is held by bifurcated NH center dot center dot center dot O center dot center dot center dot HN intermolecular bonds. A local planar symmetry is observed in the crystal for the central -SN(H)C(O)N(H)S- skeleton. Experimental and calculated data allow to trace this structural feature to the occurrence of N-H center dot center dot center dot O=C hydrogen bonding interactions. Calculated vibrational and structural properties are in good agreement with the experimentally determined features. (C) 2008 Elsevier B.V. All rights reserved.

Syntheses, crystal structure and theoretical investigation of novel heteroleptic complexes of nickel(II) with N-R-sulfonyldithiocarbimate and phosphine ligands

Five new complexes of general formula: [Ni(RSO(2)N=CS(2))(dppe)], where R = C(6)H(5) (1), 4-ClC(6)H(4) (2), 4-BrC(6)H(4) (3), 4-IC(6)H(4) (4) and dppe = 1,2-bis(diphenylphosphino) ethane and [Ni(4-IC(6)H(4)SO(2)N=CS(2))(PPh(3))(2)] (5), where PPh3 = triphenylphosphine, were obtained in crystalline form by the reaction of the appropriate potassium N-R-sulfonyldithiocarbimate K(2)(RSO(2)N=CS(2)) and dppe or PPh(3) with nickel(II) chloride in ethanol/water. The elemental analyses and the IR, (1)H NMR, (13)C NMR and (31)P NMR spectra are consistent with the formation of the square planar nickel(II) complexes with mixed ligands. All complexes were also characterized by X-ray diffraction techniques and present a distorted cis-NiS(2)P(2) square-planar configuration around the Ni atom. Quantum chemical calculations reproduced the crystallographic structures and are in accord with the spectroscopic data. Rare C-H center dot center dot center dot Ni intramolecular short contact interactions were observed in the complexes 1-5. (C) 2011 Elsevier B. V. All rights reserved.

Cyclocreatine, an anticancer and neuroprotective agent. Spectroscopic, structural and theoretical study

The structural, spectroscopic and theoretical study of cyclocreatine (1-carboxymethyl-2-iminoimidazolidine, CyCre) has been performed prompted by the biological relevance of the molecule and its potential role as a ligand in biometalic compounds. The crystal structure of CyCre has been determined by X-ray diffraction methods. The compound crystallizes as a zwitterion in the monoclinic system, space group P2(1)/c. The crystal is further stabilized by a network of N-H center dot center dot center dot O bonds. Infrared and Raman spectra of the solid, electronic spectra of aqueous solutions at different pH values and (1)H and (13)C NMR spectra have been recorded and analyzed. Band assignments were accomplished with the help of theoretical calculations. Optimized molecular geometries, harmonic vibrational frequencies and molecular electrostatic potentials were calculated using methods based on the density functional theory. (C) 2010 Elsevier B.V. All rights reserved.

Experimental and theoretical investigation of molecular structure and conformation of the 4-isopropylthioxanthone

In this study, the molecular structure and conformational analyses of the 4-isopropylthioxanthone (4-ITX) are reported according to experimental and theoretical results. The compound crystallizes in the centrosymmetric P (1) over bar space group with only one molecule in the asymmetric unit, presenting the most stable conformation, in which the three fused-rings adopt a planar geometry, and the isopropyl group assumes a torsional angle with less sterical hindrance. The structural and conformational analyses were performed using theoretical calculations such as Hartree-Fock (HF), DFT method in combination with 6-311G(d,p) and 6-31++G(d,p) and the results were compared with infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). The supramolecular assembly of 4-ITX is kept by non-classical C-H center dot center dot center dot O hydrogen bonds and weak interactions such as pi-pi stacking. 4-ITX was also studied by (1)H and (13)C NMR spectroscopy. UV-Vis absorption spectroscopic properties of the 4-ITX showed the long-wavelength maximum shifts towards high energy when the solvent polarity increases. (C) 2011 Elsevier B.V. All rights reserved.

Excited Electronic States, Transition Probabilities, and Radiative Lifetimes of CAs: A Theoretical Contribution and Challenge to Experimentalists

High-level CASSCF/MRCI calculations with a quintuple-zeta quality basis set are reported by characterizing for the first time a manifold of electronic states of the CAs radical yet to be investigated experimentally. Along with the potential energy curves and the associated spectroscopic constants, the dipole moment functions for selected electronic states as well as the transition dipole moment functions for the most relevant electronic transitions are also presented. Estimates of radiative transition probabilities and lifetimes complement this investigation, which also assesses the effect of spin-orbit interaction on the A (2)Pi state. Whenever pertinent, comparisons of similarities and differences with the isovalent CN and CP radicals are made.

Photophysics and photostability of adenine in aqueous solution: A theoretical study

The sequential Monte Carlo/CASPT2 approach was employed to investigate deactivation and emission processes from the lowest-lying pi pi * and n pi * excited states of 9H-adenine in aqueous solution. It is found that conical intersections connecting the pi pi* and n pi* states with the ground state are also present in solution, whereas the barriers for the deactivation paths are significantly smaller on solvated conditions. The large destabilization of the n pi* state found in solution possibly prevents its involvement in the deactivation photophysics and explains the change from a bi- to a mono-exponential decay for the molecule in the gas phase and solution, respectively. (C) 2010 Elsevier B.V. All rights reserved.

Designing Novel Antitrypanosomal Agents from a Mixed Graph-Theoretical Substructural Approach

Chagas disease is nowadays the most serious parasitic health problem. This disease is caused by Trypanosoma cruzi. The great number of deaths and the insufficient effectiveness of drugs against this parasite have alarmed the scientific community worldwide. In an attempt to overcome this problem, a model for the design and prediction of new antitrypanosomal agents was obtained. This used a mixed approach, containing simple descriptors based on fragments and topological substructural molecular design descriptors. A data set was made up of 188 compounds, 99 of them characterized an antitrypanosomal activity and 88 compounds that belong to other pharmaceutical categories. The model showed sensitivity, specificity and accuracy values above 85%. Quantitative fragmental contributions were also calculated. Then, and to confirm the quality of the model, 15 structures of molecules tested as antitrypanosomal compounds (that we did not include in this study) were predicted, taking into account the information on the abovementioned calculated fragmental contributions. The model showed an accuracy of 100% which means that the ""in silico"" methodology developed by our team is promising for the rational design of new antitrypanosomal drugs. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 882-894. 2010

Solvatochromic and lonochromic Effects of Iron(II)bis-(1,10-phenanthroline)dicyano: a Theoretical Study

Solvatochromic and ionochromic effects of the iron(II)bis(1,10-phenanthroline)dicyano (Fe(phen)(2)(CN)(2)) complex were investigated by means of combined DFT/TDDFT calculations using the PBE and B3LYP functionals. Extended solvation models of Fe(phen)(2)(CN)(2) in acetonitrile and aqueous solution, as well as including interaction with Mg(2+), were constructed. The calculated vertical excitation energies reproduce well the observed solvatochromism in acetonitrile and aqueous solutions, the ionochromism in acetonitrile in the presence of Mg(2+), and the absence of ionochromic effect in aqueous solution. The vertical excitation energies and the nature of the transitions were reliably predicted after inclusion of geometry relaxation upon aqueous micro- and global solvation and solvent polarization effect in the TDDFT calculations. The two intense UV-vis absorption bands occurring for all systems studied are interpreted as transitions from a hybrid Fe(II)(d)/cyano N(p) orbital to a phenanthroline pi* orbital rather than a pure metal-to-ligand-charge transfer (MLCT). The solvatochromic and ionochromic blue band shifts of Fe(phen)(2)(CN)(2) were explained with preferential stabilization of the highest occupied Fe(II)(d)/cyano N(p) orbitals as a result of specific interactions with water solvent molecules or Mg(2+) ions in solution. Such interactions occur through the CN(-) groups in the complex, and they have a decisive role for the observed blue shifts of UV-vis absorption bands.

Structural and spectroscopic properties of the diazocarbene radical (CNN) and its ions CNN(+) and CNN(-): a high-level theoretical investigation

The diazocarbene radical, CNN, and the ions CNN(+) and CNN(-) were investigated at a high level of theory. Very accurate structural parameters for the states X(3)Sigma(-) and A(3)Pi of CNN, and X(2)Pi of both CNN(+) and CNN(-) were obtained with the UCCSD(T) method using correlated-consistent basis functions with extrapolations to the complete basis set limit, with valence only and also with all electrons correlated. Harmonic and anharmonic frequencies were obtained for all species and the Renner parameter and average frequencies evaluated for the Pi states. At the UCCSD(T)/CBS(T-5) level of theory, Delta(f)H(0 K) = 138.89 kcal/mol and Delta(f)H(298 K) = 139.65 kcal/mol were obtained for diazocarbene; for the ionization potential and the electron affinity of CNN, 10.969 eV (252.95 kcal/mol), and 1.743 eV (40.19 kcal/mol), respectively, are predicted. Geometry optimization was also carried out with the CASSCF/MRCI/CBS(T-5) approach for the states X(3)Sigma(-) A(3)Pi, and a(1)Delta of CNN, and with the CASSCF/MRSDCI/aug-cc-pVTZ approach for the states b(1)Sigma(+), c(1)Pi, d(1)Sigma(-), and B(3)Sigma(-), and excitation energies (T(e)) evaluated. Vertical energies were calculated for 15 electronic states, thus improving on the accuracy of the five transitions already described, and allowing for a reliable overview of a manifold of other states, which is expected to guide future spectroscopic experiments. This study corroborates the experimental assignment for the vertical transition X (3)Sigma(-) <- E (3)Pi.

Design of novel antituberculosis compounds using graph-theoretical and substructural approaches

The increasing resistance of Mycobacterium tuberculosis to the existing drugs has alarmed the worldwide scientific community. In an attempt to overcome this problem, two models for the design and prediction of new antituberculosis agents were obtained. The first used a mixed approach, containing descriptors based on fragments and the topological substructural molecular design approach (TOPS-MODE) descriptors. The other model used a combination of two-dimensional (2D) and three-dimensional (3D) descriptors. A data set of 167 compounds with great structural variability, 72 of them antituberculosis agents and 95 compounds belonging to other pharmaceutical categories, was analyzed. The first model showed sensitivity, specificity, and accuracy values above 80% and the second one showed values higher than 75% for these statistical indices. Subsequently, 12 structures of imidazoles not included in this study were designed, taking into account the two models. In both cases accuracy was 100%, showing that the methodology in silico developed by us is promising for the rational design of antituberculosis drugs.

Spectroscopic and theoretical studies of some N-methoxy-N-methyl-2-[(4 `-substituted) phenylsulfonyl]propanamides

The analysis of the IR carbonyl band of the N-methoxy-N-methyl-2-[(4`-substituted)phenyisulfonyI]propanamides Y-PhSO(2)CH(Me)C(O)N(OMe)Me (Y = OMe 1, Me 2, H 3, Cl 4, NO(2) 5), supported by HF/6-31G(d,p) calculations of 3,, indicated the existence of two gauche conformers (g(1) and g(2)), the g, conformer being the most stable and the least polar one (in gas phase and in solution). Both conformers are present in solution of the non polar solvent (CCl(4)) for 1-5 and in solution of the more polar solvents (CHCl(3)) for 1. 4, 5 and (CH(2)Cl(2)) for 5, while only the g(1) conformer is present in solution of the most polar solvent (CH(3)CN) for 1-5. The g, and g2 conformers correspond to the enantiomeric pairs of diastereomers (diast(1) and diast(2)) whose relative configurations are [C(3)(R)N(R)]/[C(3)(s)N(s)] and [C(3)(R)N(s)]/[C(3)(s)N(R)], respectively. The computed carbonyl frequencies for g(1) (diast(1)) and g(2) (diast(2)) stereoisomers of3 match well the experimental values. The NBO analysis, for 3 shows the important role of the orbital interactions in conformer stabilization and the overall balance of these interactions corroborates that the g, conformer is more stable than the 92 one. The observed abnormal solvent effect on the relative intensities of the carbonyl doublet components is attributed to the molecular crowding in the g2 conformer which hinders its solvation in comparison to the g, conformer (diast(1)). X-ray single crystal analysis performed for 3 shows the existence Of two 92, and g(1b) conformers of diastereomers (diast2, and diast(1b)) whose absolute configurations are [C(3)(R)N(s)] and [C(3)(R)N(R)], respectively. The larger population and. thus, the larger stabilization of the g(2), conformer over the gib form in the crystals may be associated with a larger energy gain deriving from dipole moment coupling in the former conformer along with a series of C-H center dot center dot center dot O electrostatic and hydrogen bond interactions, (C) 2009 Elsevier B.V. All rights reserved.

Spectroscopic and theoretical studies of some N-methoxy-N-methyl-2-[(4 `-substituted) phenylthio]propanamides

The analysis of the IR carbonyl band of the N-methoxy-N-methyl-2-[(4`-substituted)phenylthio]propanamides Y-PhSCH(Me)C(O)N(OMe)Me (Y=OMe 1, Me 2, H 3, Cl 4, NO(2) 5), supported by B3LYP/cc-pVDZ calculations of 3, indicated the existence of two gauche conformers (g(1) and g(2)), the g(1) conformer being the more stable and the less polar one (in gas phase and in solution). Both conformers are present in solution of the polar solvents (CH(2)Cl(2) and CH(3)CN) for 1-5 and in solution of the less polar solvent (CHCl(3)) for 1-4, while only the g(1) conformer is present in solution of non polar solvents (n-C(6)H(14) and CCl(4)) and in solution of CHCl(3) for 5. NBO analysis shows that both the sigma(C-S) -> pi*(C=O) (hyperconjugative) and the pi(C=O) -> sigma*(C-S) orbital interactions contribute almost to the same extent for the stabilization of g(1) and g(2) conformers. The pi*(C=O) -> sigma*(C-S), n(S) -> pi*(C=O) and the n(S) -> pi*(C=O) orbital interactions stabilize more the g(1) conformer than the g(2) one. Moreover, the suitable geometry of the g(1) conformer leads to its stabilization through the LP(O2) -> sigma*(C8-H11) orbital interaction (hydrogen bond) along with the strong O([CO])(delta-) center dot center dot center dot H([O-Ph])(delta+) electrostatic interaction. On the other hand, the appropriate geometry of the g(2) conformer leads to its stabilization by the LP(O22) -> sigma*(C9-H13) orbital interaction (hydrogen bond) along with the weak O([OMe])(delta-) center dot center dot center dot H([o`-Ph])(delta+) electrostatic static interaction. As for the 4`-nitro derivative 5 the ortho-phenyl hydrogen atom becomes more acidic, leading to a stronger O([CO])(delta-) center dot center dot center dot H([o-Ph])(delta+) interaction and, thus, into a larger stabilization of the g(1) conformer in the whole series. This trend is responsible for the unique IR carbonyl band in CHCl(3) solution of 5. The larger occupancy of the pi*(C=O) orbital of the g(1) conformer relative to that of the g(2) conformer, along with the O([CO])(delta-) center dot center dot center dot H([o-Ph])(delta+) electrostatic interaction (hydrogen bond) justifies the lower carbonyl frequency of the g(1) conformer with respect to the g(2) one, in gas phase and in solution. (C) 2008 Elsevier B.V. All rights reserved.

Theoretical Characterization of Hydrogen Polyoxides: HOOH, HOOOH, HOOOOH, and HOOO

We have investigated the polyoxides HOOH, HOOOH, HOOOOH, and HOOO employing the CCSD(T) methodology, and the correlation consistent basis sets. For all molecules, we have computed fundamental vibrational frequencies, structural parameters, rotational constants, and rotation-vibration corrections. For HOOOH, we have obtained a good agreement between our results and microwave and infrared spectra measurements, although for the symmetric OO stretch some important differences were found. Heats of formation were computed using atomization energies, and our recommendation is as follows: Delta H degrees(f,298)(HOOOH) = -21.50 kcal/mol and Delta H degrees(f,298)(HOOOOH) = -10.61 kcal/mol. In the case of HOOO, to estimate the heat of formation, we have constructed three isodesmic reactions to cancel high order correlation effects. The results obtained confirmed that the latter effects are very important for HOOO. The new Delta H degrees(f,298)(HOOO) obtained is 5.5 kcal/mol. We have also calculated the zero-point energies of DO and DOOO to correct the experimental lower limit determined for the Delta H degrees(f,298)(HOOO). The Delta(Delta ZPE) decreases the binding energy of HOOO by 0.56 kcal/mol. Employing the latter value, the new experimental lower limit for Delta H degrees(f,298)(HOOO) is 3.07 kcal/mol, just 2.4 kcal/mol lower than our determination. We expect that the fundamental vibrational frequencies and rotational constants determined for HOOOOH and DOOOOD contribute to its identification in the gas phase. The vibrational spectrum of HOOOOH shows some overlapping with that of HOOOH thus indicating that one may encounter some difficulties in its characterization. We discuss the consequences of the thermochemical properties determined in this work, and suggest that the amount of HOOO present in the atmosphere is smaller than that proposed recently in this journal (J. Phys. Chem A 2007, 111, 4727).

Electronic structure and spectra of a new molecular species: SI. A theoretical contribution

A high level theoretical approach is used to characterize for the first time a manifold of doublet and quartet A + S and Omega states correlating with the first two dissociation channels of an as yet experimentally unknown molecular species, SI, sulfur monoidide. A set of spectroscopic constants is determined, including vibrationally averaged spin-orbit coupling constants, vibrationally averaged dipole moments, and dissociation energies. The transition dipole moment function for the spin-forbidden transition a (4)Sigma -X (2)Pi, and the associated radiative lifetimes were also evaluated. Two possibilities to detect transitions experimentally and to derive spectroscopic constants are suggested. (C) 2011 Elsevier B. V. All rights reserved.

2-Aminopurine non-radiative decay and emission in aqueous solution: A theoretical study

The minimum energy path along the lowest-lying pi pi* excited state of 2-aminopurine was calculated to elucidate the mechanisms of radiationless decay and emission in water. The sequential Monte Carlo quantum mechanics approach with a multiconfigurational and perturbative description of the wave function was employed to compute the minimum, transition state, and conical intersection. It was found that the barrier in the potential energy surface to access the conical intersection funnel increases in aqueous environment, making the system prone to enlarge the emission yield. These results rationalize the observed enhancement of emission in 2-aminopurine upon increasing of the solvent polarity. (c) 2008 Elsevier B.V. All rights reserved.