Biomedical subjects

Manuel E Minas da Piedade

Publications and source records attributed to Manuel E Minas da Piedade.

7 recordsLinked to original sources

PubMed2006

An all-atom force field for metallocenes.

A new all-atom force field, for the molecular modeling of metallocenes was constructed. Quantum chemical calculations were performed to obtain several force field terms not yet defined in the literature. The remainder were transferred from the OPLS-AA/AMBER framework. The parametrization work included the obtention of geometrical parameters, torsion energy profiles, and distributions of atomic charges that blend smoothly with the OPLS-AA specification for a variety of organic molecular fragments. Validation was carried out by comparing simulated and experimental data for five different ferrocene derivatives in the crystalline phase. The present model can be regarded as a step toward a general force field for metallocenes, built in a systematic way, easily integrated with OPLS-AA, and transferable between different metal-ligand combinations.

Journal Article↗

PubMed2006

Effect of ring substitution on the S-H bond dissociation enthalpies of thiophenols. An experimental and computational study.

There are conflicting reports on the origin of the effect of Y substituents on the S-H bond dissociation enthalpies (BDEs) in 4-Y-substituted thiophenols, 4-YC(6)H(4)S-H. The differences in S-H BDEs, [4-YC(6)H(4)S-H] - [C(6)H(5)S-H], are known as the total (de)stabilization enthalpies, TSEs, where TSE = RSE - MSE, i.e., the radical (de)stabilization enthalpy minus the molecule (de)stabilization enthalpy. The effects of 4-Y substituents on the S-H BDEs in thiophenols and on the S-C BDEs in phenyl thioethers are expected to be almost identical. Some S-C TSEs were therefore derived from the rates of homolyses of a few 4-Y-substituted phenyl benzyl sulfides, 4-YC(6)H(4)S-CH(2)C(6)H(5), in the hydrogen donor solvent 9,10-dihydroanthracene. These TSEs were found to be -3.6 +/- 0.5 (Y = NH(2)), -1.8 +/- 0.5 (CH(3)O), 0 (H), and 0.7 +/- 0.5 (CN) kcal mol(-1). The MSEs of 4-YC(6)H(4)SCH(2)C(6)H(5) have also been derived from the results of combustion calorimetry, Calvet-drop calorimetry, and computational chemistry (B3LYP/6-311+G(d,p)). The MSEs of these thioethers were -0.6 +/- 1.1 (NH(2)), -0.4 +/- 1.1 (CH(3)O), 0 (H), -0.3 +/- 1.3 (CN), and -0.8 +/- 1.5 (COCH(3)) kcal mol(-1). Although all the enthalpic data are rather small, it is concluded that the TSEs in 4-YC(6)H(4)SH are largely governed by the RSEs, a somewhat surprising conclusion in view of the experimental fact that the unpaired electron in C(6)H(5)S(*) is mainly localized on the S. The TSEs, RSEs, and MSEs have also been computed for a much larger series of 4-YC(6)H(4)SH and 4-YC(6)H(4)SCH(3) compounds by using a B3P86 methology and have further confirmed that the S-H/S-CH(3) TSEs are dominated by the RSEs. Good linear correlations were obtained for TSE = rho(+)sigma(p)(+)(Y), with rho(+) (kcal mol(-1)) = 3.5 (S-H) and 3.9 (S-CH(3)). It is also concluded that the SH substituent is a rather strong electron donor with a sigma(p)(+)(SH) of -0.60, and that the literature value of -0.03 is in error. In addition, the SH rotational barriers in 4-YC(6)H(4)SH have been computed and it has been found that for strong electron donating (ED) Ys, such as NH(2), the lowest energy conformer has the S-H bond oriented perpendicular to the aromatic ring plane. In this orientation the SH becomes an electron withdrawing (EW) group. Thus, although the OH group in phenols is always in-plane and ED irrespective of the nature of the 4-Y substituent, in thiophenols the SH switches from being an ED group with EW and weak ED 4-Ys, to being an EW group for strong ED 4-Ys.

Journal Article↗

PubMed2006

Energetics of the thermal dimerization of acenaphthylene to heptacyclene.

The energetics of the thermal dimerization of acenaphthylene to give Z- or E-heptacyclene was investigated. The standard molar enthalpy of the formation of monoclinic Z- and E-heptacyclene isomers at 298.15 K was determined as Delta(f)H(m)o (E-C24H16, cr) = 269.3 +/- 5.6 kJ x mol(-1) and Delta(f)H(m)o (Z-C24H16, cr) = 317.7 +/- 5.6 kJ x mol(-1), respectively, by microcombustion calorimetry. The corresponding enthalpies of sublimation, Delta(sub)H(m)o (E-C24H16) = (149.0 +/- 3.1) kJ x mol(-1) and Delta(sub)H(m)o (Z-C24H16) = (128.5 +/- 2.3) kJ x mol(-1) were also obtained by Knudsen effusion and Calvet-drop microcalorimetry methods, leading to Delta(f)H(m)o (E-C24H16, g) = (418.3 +/- 6.4) kJ x mol(-1) and Delta(f)H(m)o (Z-C24H16, g) = (446.2 +/- 6.1) kJ x mol(-1), respectively. These results, in conjunction with the reported enthalpies of formation of solid and gaseous acenaphthylene, and the entropies of acenaphthylene and both hepatcyclene isomers obtained by the B3LYP/6-31G(d,p) method led to the conclusion that at 298.15 K the thermal dimerization of acenaphthylene is considerably exothermic and exergonic in the solid and gaseous states (although more favorable when the E isomer is the product), suggesting that the nonobservation of the reaction under these conditions is of kinetic nature. A full determination of the molecular and crystal structure of the E dimer by X-ray diffraction is reported for the first time. Finally, molecular dynamics computer simulations on acenaphthylene and the heptacyclene solids were carried out and the results discussed in light of the corresponding structural and Delta(sub)H(m)o data experimentally obtained.

Journal Article↗

PubMed2005

A molecular dynamics study of the thermodynamic properties of calcium apatites. 1. Hexagonal phases.

Structural and thermodynamic properties of crystal hexagonal calcium apatites, Ca10(PO4)6(X)2 (X = OH, F, Cl, Br), were investigated using an all-atom Born-Huggins-Mayer potential by a molecular dynamics technique. The accuracy of the model at room temperature and atmospheric pressure was checked against crystal structural data, with maximum deviations of ca. 4% for the haloapatites and 8% for hydroxyapatite. The standard molar lattice enthalpy, delta(lat)H298(o), of the apatites was calculated and compared with previously published experimental results, the agreement being better than 2%. The molar heat capacity at constant pressure, C(p,m), in the range 298-1298 K, was estimated from the plot of the molar enthalpy of the crystal as a function of temperature, H(m) = (H(m,298) - 298C(p,m)) + C(p,m)T, yielding C(p,m) = 694 +/- 68 J x mol(-1) x K(-1), C(p,m) = 646 +/- 26 J x mol(-1) x K(-1), C(p,m) = 530 +/- 34 J x mol(-1) x K(-1), and C(p,m) = 811 +/- 42 J x mol(-1) x K(-1) for hydroxy-, fluor-, chlor-, and bromapatite, respectively. High-pressure simulation runs, in the range 0.5-75 kbar, were performed in order to estimate the isothermal compressibility coefficient, kappaT, of those compounds. The deformation of the compressed solids is always elastically anisotropic, with BrAp exhibiting a markedly different behavior from those displayed by HOAp and ClAp. High-pressure p-V data were fitted to the Parsafar-Mason equation of state with an accuracy better than 1%.

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PubMed2005

Energetics of hydroxybenzoic acids and of the corresponding carboxyphenoxyl radicals. Intramolecular hydrogen bonding in 2-hydroxybenzoic acid.

The energetics of the phenolic O-H bond in the three hydroxybenzoic acid isomers and of the intramolecular hydrogen O-H- - -O-C bond in 2-hydroxybenzoic acid, 2-OHBA, were investigated by using a combination of experimental and theoretical methods. The standard molar enthalpies of formation of monoclinic 3- and 4-hydroxybenzoic acids, at 298.15 K, were determined as Delta(f)(3-OHBA, cr) = -593.9 +/- 2.0 kJ x mol(-1) and Delta(f)(4-OHBA, cr) = -597.2 +/- 1.4 kJ x mol(-1), by combustion calorimetry. Calvet drop-sublimation calorimetric measurements on monoclinic samples of 2-, 3-, and 4-OHBA, led to the following enthalpy of sublimation values at 298.15 K: Delta(sub)(2-OHBA) = 94.4 +/- 0.4 kJ x mol(-1), Delta(sub)(3-OHBA) = 118.3 +/- 1.1 kJ x mol(-1), and Delta(sub)(4-OHBA) = 117.0 +/- 0.5 kJ x mol(-1). From the obtained Delta(f)(cr) and Delta(sub) values and the previously reported enthalpy of formation of monoclinic 2-OHBA (-591.7 +/- 1.3 kJ x mol(-1)), it was possible to derive Delta(f)(2-OHBA, g) = -497.3 +/- 1.4 kJ x mol(-1), Delta(f)(3-OHBA, g) = -475.6 +/- 2.3 kJ x mol(-1), and Delta(f)(4-OHBA, cr) = -480.2 +/- 1.5 kJ x mol(-1). These values, together with the enthalpies of isodesmic and isogyric gas-phase reactions predicted by density functional theory (B3PW91/aug-cc-pVDZ, MPW1PW91/aug-cc-pVDZ, and MPW1PW91/aug-cc-pVTZ) and the CBS-QMPW1 methods, were used to derive the enthalpies of formation of the gaseous 2-, 3-, and 4-carboxyphenoxyl radicals as (2-HOOCC(6)H(4)O(*), g) = -322.5 +/- 3.0 kJ.mol(-1) Delta(f)(3-HOOCC(6)H(4)O(*), g) = -310.0 +/- 3.0 kJ x mol(-1), and Delta(f)(4-HOOCC(6)H(4)O(*), g) = -318.2 +/- 3.0 kJ x mol(-1). The O-H bond dissociation enthalpies in 2-OHBA, 3-OHBA, and 4-OHBA were 392.8 +/- 3.3, 383.6 +/- 3.8, and 380.0 +/- 3.4 kJ x mol(-1), respectively. Finally, by using the ortho-para method, it was found that the H- - -O intramolecular hydrogen bond in the 2-carboxyphenoxyl radical is 25.7 kJ x mol(-1), which is ca. 6-9 kJ x mol(-1) above the one estimated in its parent (2-OHBA), viz. 20.2 kJ x mol(-1) (theoretical) or 17.1 +/- 2.1 kJ x mol(-1) (experimental).

Crystallography, X-Ray↗

PubMed2003

Bonding energetics in alkaline metal alkoxides and phenoxides.

The bonding energetics in a variety of alkaline metal, alkoxides and phenoxides, MOR, was investigated based on the corresponding enthalpies of formation in the crystalline state determined by reaction-solution calorimetry. The results obtained at 298.15 K were as follows: Delta(f)H(m)(o)(MOR, cr)/kJ mol(-1) = 382.7+/-1.4 (LiOC(6)H(5)), 513.6+/-2.5 (NaO-nC(6)H(13)), 326.4+/-1.4 (NaOC(6)H(5)), 375.2+/-3.4 (KOCH(3)), 434.5+/-2.7 (KOC(2)H(5)), 467.1+/-5.2 (KO-nC(3)H(7)), 459.3+/-2.1 (KO-nC(4)H(9)), 464.6+/-5.7 (KO-tC(4)H(9)), 464.3+/-2.5 (KO-nC(6)H(13)), 333.3+/-3.1 (KOC(6)H(5)), 380.6+/-2.9 (RbOCH(3)), 434.1+/-2.9 (RbOC(2)H(5)), 345.3+/-2.9 (LiOC(6)H(5)), 379.1+/-3.0 (CsOCH(3)), 432.3+/-3.1 (CsOC(2)H(5)), 466.9+/-5.0 (CsO-nC(3)H(7)), 461.3+/-3.5 (CsO-nC(4)H(9)), 461.9+/-2.5 (CsO-tC(4)H(9)), 349.2+/-1.4 (CsOC(6)H(5)). These results together with revised Delta(f)H(m)(o)(MOR, cr) values from the literature, were used to derive a consistent set of lattice energies for the MOR compounds and discuss general trends in the structure-energetics relationship based on the Kapustinskii equation.

Journal Article↗

PubMed2002

The aromaticity of pyracylene: an experimental and computational study of the energetics of the hydrogenation of acenaphthylene and pyracylene.

In this work, the aromaticity of pyracylene (2) was investigated from an energetic point of view. The standard enthalpy of hydrogenation of acenaphthylene (1) to acenaphthene (3) at 298.15 K was determined to be minus sign(114.5 +/- 4.2) kJ x mol(-1) in toluene solution and minus sign(107.9 +/- 4.2) kJ x mol(-1) in the gas phase, by combining results of combustion and reaction-solution calorimetry. A direct calorimetric measurement of the standard enthalpy of hydrogenation of pyracylene (2) to pyracene (4) in toluene at 298.15 K gave -(249.9 plus minus 4.6) kJ x mol(-1). The corresponding enthalpy of hydrogenation in the gas phase, computed from the Delta(f)H(o)m(cr) and DeltaH(o)m(sub) values obtained in this work for 2 and 4, was -(236.0 +/- 7.0) kJ x mol(-1). Molecular mechanics calculations (MM3) led to Delta(hyd)H(o)m(1,g) = -110.9 kJ x mol(-1) and Delta(hyd)H(o)m(2,g) = -249.3 kJ x mol(-1) at 298.15 K. Density functional theory calculations [B3LYP/6-311+G(3d,2p)//B3LYP/6-31G(d)] provided Delta(hyd)H(o)m(2,g) = -(244.6 +/- 8.9) kJ x mol(-1) at 298.15 K. The results are put in perspective with discussions concerning the "aromaticity" of pyracylene. It is concluded that, on energetic grounds, pyracylene is a borderline case in terms of aromaticity/antiaromaticity character.

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