Manuel Montejo

Theoretical and experimental vibrational spectrum study of 4-hydroxybenzoic acid as monomer and dimer.

Theoretical calculations on the molecular geometry and the vibrational spectrum of 4-hydroxybenzoic acid were carried out by the Density Functional Theory (DFT/B3LYP) method. In addition, IR and Raman spectra of the 4-hydroxybenzoic acid in solid phase were newly recorded using them in conjunction the experimental and theoretical data (including SQM calculations), a vibrational analysis of this molecular specie was accomplished and a reassignment of the normal modes corresponding to some spectral bands was proposed. The geometries of monomers and dimers in gas phase were optimized using the DFT B3LYP method with the 6-31G*, D95** and 6-311++G** basis sets. Also, both the vibrational spectra recorded and the results of the theoretical calculations show the presence of one stable conformer for the 4-hydroxybenzoic acid cyclic dimer. The B3LYP/6-31G* method was used to study the structure for cyclic dimer of 4-hydroxybenzoic acid and for a complete assignment our results were compared with results of the cyclic dimer of benzoic acid. A scaled quantum mechanical analysis was carried out to yield the best set of harmonic force constants. The formation of the hydrogen bond was investigated in terms of the charge density by the AIM program and by the NBO calculations.

Triethylsilanol: molecular conformations and role of the hydrogen-bonding oligomerization in its vibrational spectra.

We report a theoretical study of the molecular structure of the triethylsilanol molecule and a thorough conformational analysis of the species following the Boltzmanns distribution law. The vibrational spectra of the title molecule have been assigned by means of the combined use of experimental data obtained from IR and Raman spectra and theoretical DFT calculations with the subsequent implementation of the SQMFF methodology. The role of hydrogen bonding in the shifting of the vibrational bands of the silanol group in the spectra of the liquid phase is discussed using a model of triethylsilanol dimer.

Vibrational circular dichroism and theoretical study of the conformational equilibrium in (-)-S-nicotine.

We report an extensive study of the molecular and electronic structure of (-)-S-nicotine, to deduce the phenomenon that controls its conformational equilibrium and to solve its solution-state conformer population. Density functional theory, ab initio, and molecular mechanics calculations were used together with vibrational circular dichroism (VCD) and Fourier transform infrared spectroscopies. Calculations and experiments in solution show that the structure and the conformational energy profile of (-)-S-nicotine are not strongly dependent on the medium, thus suggesting that the conformational equilibrium is dominated by hyperconjugative interactions rather than repulsive electronic effects. The analysis of the first recorded VCD spectra of (-)-S-nicotine confirmed the presence of two main conformers at room temperature. Our results provide further evidence of the hypersensitivity of vibrational optical activity spectroscopies to the three-dimensional structure of chiral samples and prove their suitability for the elucidation of solution-state conformer distribution.

Quantum chemical study of silanediols as metal binding groups for metalloprotease inhibitors

DFT (B3LYP and M06L) as well as ab initio (MP2) methods with Dunning cc-pVnZ (n = 2,3) basis sets are employed for the study of the binding ability of the new class of protease inhibitors, i.e., silanediols, in comparison to the well-known and well-studied class of inhibitors with hydroxamic functionality (HAM). Active sites of metalloproteases are modeled by [R3M-OH2]2+ complexes, where R stands for ammonia or imidazole molecules and M is a divalent cation, namely zinc, iron or nickel (in their different spin states). The inhibiting activity is estimated by calculating Gibbs free energies of the water displacement by metal binding groups (MBGs) according to: [R3M-OH2]2+ + MBG → [R3M-MBG]2+ + H2O. The binding energy of silanediol is only a few kcal mol−1 inferior to that of HAM for zinc and iron complexes and is even slightly higher for the triplet state of the (NH3)3Ni2+ complex. For both MBGs studied in the ammonia model the binding ability is nearly the same, i.e., Fe2+(t) > Ni2+(t) > Fe2+(q) > Ni2+(s) > Zn2+. However, for the imidazole model the order is slightly different, i.e., Ni2+(t) > Fe2+(t) > Fe2+(q) > Ni2+(s) ≥ Zn2+. Equilibrium structures of the R3Zn 2+ complexes with both HAM and silanediol are characterized by the monodentate binding, but the bidentate character of binding increases on going to iron and nickel complexes. Two types of intermediates of the water displacement reactions for [(NH3)3M-OH2]2+ complexes were found which differ by the direction of the attack of the MBG. Hexacoordinated complexes exhibit bidentate bonding of MBGs and are lower in energy for M=Ni and Fe. For Zn penta- and hexacoordinated complexes have nearly the same energy. Intermediate complexes with imidazole ligands have only octahedral structures with bidentate bonding of both HAM and dimethylsilanediol molecules.

An experimental and theoretical study of the molecular structure and vibrational spectra of iodotrimethylsilane (SiIMe3)

The gas-phase molecular structure of iodotrimethylsilane (ITMS) has been determined from electron diffraction data. Infrared and Raman spectra have been completely assigned. The experimental work is supported by ab initio HF and MP2 calculations for the gas-phase structure determination and DFT(B3LYP) calculations, combined with Pulays SQM method, for the vibrational spectra data.

DFT study of the hydrolysis reaction in atranes and ocanes: the influence of transannular bonding

AbstractThermochemical kinetics of hydrolysis reactions of compounds with transannular intramolecular M…N bonds, i.e., atranes RM(OCH2CH2)3N and ocanes R2M(OCH2CH2)2NH (M = Si, Ge; R = F, Cl, Me), is studied at the B3LYP/aug-cc-pVDZ theoretical level. Several DFT methods are assessed for the reproduction of the experimental activation barrier for the Si-O bond cleavage of 1-methylsilatrane. Activation barriers for atranes and ocanes show the tendency for their growth with the decrease of the electronegativity of a substituent R on going from F to Me and their decrease from Si to Ge. Hydrolysis activation barriers of atranes and ocanes are compared with those of their acyclic analogs RM(OCH3)3 and R2M(OCH2)2NH in order to study the role of transannular M…N bonds in the stability of these molecules to hydrolysis. Substantially larger barriers for atranes support the opinion that stability of atranes may be explained by the formation of intramolecular bonds; however, the strengthening of transannular M…N bonds results in lower M-O cleavage barriers. It was proposed that the M-O cleavage barrier height is determined not by a weak M…N bonding itself, but rather by the contribution of a nitrogen lone pair to the antibonding orbitals of M-O bonds. The NBO analysis show that this interaction increases with the decrease of the electronegativity of a substituent R and decreases on going from atranes to ocanes. In ocanes, the presence of M…N bonds does not kinetically hinder the hydrolytic process; M-O cleavage activation barriers for acyclic analogs are higher. M-Hal cleavage barriers are substantially higher than those for M-O cleavage for R = F, but lower for R = Cl. Graphical AbstractThe experimental barrier height of the Si-O bond cleavage in 1-methylsilatrane is well reproduced when three explicit water molecules are included in the B3LYP/aug-cc-pVDZ theoretical model.

Interaction models of the Si(OH)2 functionality with Zn2+ cation in simplified biological environments: a DFT study

We report a DFT study (M06L/cc-pVDZ) of the interactions between the Si(OH)2 group in three simplified gem-silanediols [i.e., N-[dihydroxy(methyl)silyl] methyl}formamide (DHSF), 3-[dihydroxy (methyl) silyl] propanamide (DHSP), and 3,3′-(dihydroxysilanediyl)dipropanamide (DHSDP)], which have a similar structure to silanediol-based inhibitors of metalloproteases, and simplified active site models: [Zn(Imdz)3–OH2]2+ and [Zn(Imdz)2R–OH2]2+, where R can be a formaldehyde, an acetone, or an acetic acid molecule. These models partly resemble the structure of the first coordination sphere of some metalloproteases (e.g., angiotensin I converting enzyme and thermolysin). Different types of bonding patterns were found for the systems into study. The three related silanediols may coordinate with the zinc dication in monodentate, pseudo-bidentate, and pseudo-tridentate way. Pseudo-bidentate interaction was reported to be that corresponding to the silanediol transition-state-analog of the thermolysin enzyme as confirmed by the X-ray structural study (Juers et al., Biochemistry 44:16524–16528, 2005). The binding ability of the mentioned silanediols was determined as the energy of the water displacement reaction for the mentioned active sites models in gas phase and in water solution (PCM model). The calculated binding energies point out to the higher strength of the pseudo-bidentate Zn2+–MBG interaction. Moreover, DHSDP ligand is calculated to be the strongest MBG for Zn2+ in both active sites models. NBO population analysis and the AIM methodology were implemented as a tool for evaluating electronic structure of the complexes. The results obtained may point out to the fact that the higher the electronic delocalization around the metal center is, the stronger the interaction between the MBG and the active site, bringing about a higher binding energy.

Mechanism of the Catalytic Activity of Nucleophiles in the Stepwise Hydrolysis and Condensation Reactions of Tetramethoxysilane

Active ingredients: A model for the simplest hydrolysis reaction is applied to all stages of stepwise hydrolysis and condensation taking place during a sol-gel process. The picture shows the molecular structures of the transition states of the ammonia- (left) and OH(-)-promoted (right) condensation reactions of two Si(OH)(4) molecules, including an additional water molecule.The previously proposed model of the catalytic activity of nucleophiles in the hydrolysis reaction of tetramethoxysilane is expanded to the subsequent stages of hydrolysis, that is, the stepwise hydrolysis of (MeO)(4-x)(OH)(x)Si (x=1-3) molecules, and to the condensation reaction of completely hydrolysed species. The estimate of the reaction barrier heights by using the B3LYP and MP2 methods with correlation-consistent double-zeta basis sets allows us to predict the catalytic activity of bases for the different steps of hydrolysis and for condensation reactions. In general, the catalytic activity of bases decreases with the number of hydrolysed groups, vanishing in the case of ammonia at x=2 and remaining in the case of the hydroxyl anion up to x=3. In addition, the value of the catalytic activity of NH(3) and OH(-) is of the same order of magnitude for hydrolysis reactions, while the effect of the OH(-) anion substantially exceeds that of NH(3) for condensation reactions.

A reinvestigation of the ν7 and ν10 modes of pyridazine on the basis of the inelastic neutron scattering spectrum analysis

Abstract The inelastic neutron scattering (INS) spectrum of pyridazine has been analyzed by fitting different harmonic force fields: MP2/6-311G**, BLYP/6-31G* and B3LYP/6-31G* levels, and B3LYP/6-31G* previously scaled. The four intramolecular potentials have been refined to minimise the difference between observed and calculated spectra. In all the cases, only the diagonal force constants expressed in symmetry coordinates were fitted. The combined use of wavenumbers and INS intensities in the refinement procedure has been decisive in order to clarify the assignment of the whole of the vibrational spectrum, particularly the assignment of the ν7 and ν10 modes. The INS spectrum has been analyzed using the C limax program, and a set of independent symmetry coordinates (C2v) for describing the normal modes of the pyridazine molecule. The a priori scaled B3LYP/6-31G* force field gave the best agreement with the measured INS spectral profile.

DFT‐Aided Vibrational Circular Dichroism Spectroscopy Study of (−)‐S‐cotinine

The implementation of a strategy comprising the use of vibrational circular dichroism spectroscopy and DFT calculations allows determination of the solution-state conformational distribution in (-)-S-cotinine, giving further proof of the extra conformer-discriminating potential of this experimental technique, which may offer unique molecular fingerprints of subtly dissimilar molecular conformers of chiral samples. Natural bond orbital electronic structure calculations of the rotational barrier height between the two main conformers of the species indicate that hyperconjugative effects are the key force governing the conformational equilibrium. The negligible effect of the solvents polarity over both structure and conformational energy profile supports this result.