Vibrational Dynamics of Crystalline 4-Phenylbenzaldehyde from INS Spectra and Periodic DFT Calculations.

The present work emphasizes the value of periodic density functional theory (DFT) calculations in the assessment of the vibrational spectra of molecular crystals. Periodic calculations provide a nearly one-to-one match between the calculated and observed bands in the inelastic neutron scattering (INS) spectrum of crystalline 4-phenylbenzaldehyde, thus validating their assignment and correcting previous reports based on single molecule calculations. The calculations allow the unambiguous assignment of the phenyl torsional mode at ca. 118-128 cm-1, from which a phenyl torsional barrier of ca. 4000 cm-1 is derived, and the identification of the collective mode involving the antitranslational motion of CH···O bonded pairs, a hallmark vibrational mode of systems where C-H···O contacts are an important feature.

FTIR Spectroscopy and DFT Calculations to Probe the Kinetics of ß-Carotene Thermal Degradation.

The thermal degradation of ß-carotene in air was investigated. The sample was heated at different temperatures (90, 100, 115, and 130 °C) for periods of up to 8 h to perform a complete kinetic study, the product analysis having been carried out via infrared spectroscopy in attenuated total reflectance mode coupled to density functional theory (DFT) calculations. The kinetics of this thermal degradation process was found to follow a first-order scheme, with rate coefficients varying from k90 °C = (2.0 ± 0.3) × 10-3 to k130 °C = (11.0 ± 0.7) × 10-3 min-1, the experimental activation energy having been calculated as (52 ± 1) kJ mol-1. This Ea value is close to the DFT energies corresponding to a C15-15' or a C13-14 cis-trans isomerization, followed by the formation of a carotene-oxygen diradical, which was characterized for the first time. Comparison between the experimental and calculated infrared data confirmed the C15-15'- cis rupture as the predominant reaction pathway and retinal as the major degradation product.

Novel Insights into Corema album Berries: Vibrational Profile and Biological Activity.

This study reports an evaluation of the biological properties of the edible berries from Corema album, an endemic shrub of the Portuguese coastline, aiming at its use as a nutraceutical. Different methanolic extracts were obtained from the pulp and seed of fresh berries: pulp extract, seed residue, and seed oil (extracted and characterized for the first time). For each of these, the antioxidant activity was assessed, by different methods, as well as the antimicrobial ability. Overall, the seeds were shown to be the most nutraceutical part of the berry since they showed higher antioxidant activity, while the pulp extract displayed a significant antimicrobial capacity against several clinically relevant bacterial strains. Furthermore, the extracts were fully characterized by complementary infrared and Raman spectroscopy, revealing the presence of phenolic acids, polysaccharides, sugars, and triterpenoids in the pulp, high content of unsaturated fatty acids in the seed oil, and significant amounts of phenolics and carotenoids in the seed residue. These results pave the way for a reliable correlation between chemical composition and biological activity, in edible fruit samples.

New Insights on the Vibrational Dynamics of 2-Methoxy-, 4-Methoxy- and 4-Ethoxy-Benzaldehyde from INS Spectra and Periodic DFT Calculations.

The dynamics of 2-methoxybenzaldehyde, 4-methoxybenzaldehyde, and 4-ethoxybenzaldehyde in the solid state are assessed through INS spectroscopy combined with periodic DFT calculations. In the absence of experimental data for 4-ethoxybenzaldehyde, a tentative crystal structure, based on its similarity with 4-methoxybenzaldehyde, is considered and evaluated. The excellent agreement between calculated and experimental spectra allows a confident assignment of the vibrational modes. Several spectral features in the INS spectra are unambiguously assigned and torsional potential barriers for the methyl groups are derived from experimental frequencies. The intramolecular nature of the potential energy barrier for methyl rotation about O-CH3 bonds compares with the one reported for torsion about saturated C-CH3 bonds. On the other hand, the intermolecular contribution to the potential energy barrier may represent 1/3 of the barrier height in these systems.

Conformational and vibrational study of cis-diamminedichloropalladium(II).

A conformational and vibrational analysis of cis-diamminedichloropalladium(ii) (cDDPd) is reported. Several theoretical methods (from Hartree-Fock to Møller-Plesset and Density Functional Theory) combined with different all-electron basis-sets are evaluated, in view of determining the best suited strategy for accurately representing this molecule. This choice is based on the best compromise between accuracy and computational requirements. Different scaling models were tested for obtaining the best scaling schemes of the vibrational modes to be used in this type of inorganic systems. The structural parameters and vibrational results predicted by the calculations are compared with the corresponding experimental data, namely X-ray structure and vibrational spectra. Finally, a complete assignment of the cDDPd vibrational spectra is presented.

Use of effective core potential calculations for the conformational and vibrational study of platinum(II) anticancer drugs. cis-Diamminedichloroplatinum(II) as a case study.

In the light of the recognized anticancer properties of cisplatin-type inorganic systems, the exact knowledge of their conformational preferences is of the utmost importance for understanding their biological activity. The present study reports the use of theoretical (quantum mechanical) calculations for achieving this goal. An alternative calculation method to the use of the AE basis sets, both accurate and computationally feasible, was presently tested for the conformational and vibrational study of cis-diamminedichloroplatinum(II). Effective core potentials (ECPs) were used, within the HF methodology and, within the B3LYP and mPW1PW DFT protocols. The DFT methods (particularly mPW1PW) were found to be the best choice for describing cDDP (as compared to the HF methodology).

Understanding the vibrational spectra of crystalline isoniazid: Raman, IR and INS spectroscopy and solid-state DFT study.

This work presents a comprehensive spectroscopic analysis of crystalline isoniazid, one of the main drugs in tuberculosis chemotherapy, using a blend of spectroscopic and computational methods. Mid- and far-infrared, Raman, and inelastic neutron scattering spectroscopies, with contribution of isotopic substitution are combined with discrete and periodic DFT quantum chemical calculations. This combined approach successfully reproduces the whole spectral range, allowing a sound assignment of all the vibrational bands. Previous misassignments have been corrected and several spectral features of isoniazid crystal are reported for the first time. Virtues and limitations of the computational approach (periodic and discrete) are also discussed in light of the present state-of-the-art in the field.

Probing pseudopolymorphic transitions in pharmaceutical solids using Raman spectroscopy: hydration and dehydration of theophylline.

Theophylline is known to undergo vapor phase induced hydrate-anhydrate pseudopolymorphic transformations, which can affect its bioavailability. In this work, the kinetics of the pseudopolymorphic transitions of theophylline crystals in different storage conditions is studied using a vibrational spectroscopic technique. While the hydration is a single-step process with a half-life time of ca. 5 h, the dehydration occurs through a two-step mechanism. In addition, the phase stability of hydrate-anhydrate systems in different relative humidity (RH) conditions was probed. The critical RH for anhydrous teophylline was found to be at ca. 79%, while the critical RH for dehydration is ca. 30%.

Conformational and vibrational reassessment of solid paracetamol.

This work provides an answer to the urge for a more detailed and accurate knowledge of the vibrational spectrum of the widely used analgesic/antipyretic drug commonly known as paracetamol. A comprehensive spectroscopic analysis - including infrared, Raman, and inelastic neutron scattering (INS) - is combined with a computational approach which takes account for the effects of intermolecular interactions in the solid state. This allows a full reassessment of the vibrational assignments for Paracetamol, thus preventing the propagation of incorrect data analysis and misassignments already found in the literature. In particular, the vibrational modes involving the hydrogen-bonded NH and OH groups are correctly reallocated to bands shifted by up to 300cm-1 relatively to previous assignments.

Use of FTIR, FT-Raman and 13C-NMR spectroscopy for identification of some seaweed phycocolloids.

Many seaweeds produce phycocolloids, stored in the cell wall. Members of the Rhodophyceae produce polysaccharides the main components of which are galactose (galactans)-agar and carrageenan. In addition, alginic acid is extracted from members of the Phaeophyceae. This is a binary polyuronide made up of mannuronic acid and guluronic acid. The wide uses of these phycocolloids are based on their gelling, viscosifying and emulsifying properties, which generate an increasing commercial and scientific interest. In this work, the FTIR and FT-RAMAN spectra of carrageenan and agar, obtained by alkaline extraction from different seaweeds (e.g. Mastocarpus stellatus, Chondrus crispus, Calliblepharis jubata, Chondracanthus acicularis, Chondracanthus teedei and Gracilaria gracilis), were recorded in order to identify the type of phycocolloid produced. The spectra of commercial carrageenan, alginic acid and agar samples (SIGMA and TAAB laboratories) were used as references. Special emphasis was given to the 500-1500 cm(-1) region, which presents several vibrational modes, sensitive to the type of polysaccharide and to the type of glycosidic linkage. The FT-Raman spectra present a higher resolution than FTIR spectra, this allowing the identification of a larger number of characteristic bands. In some cases, phycocolloids can be identified by FT-Raman spectroscopy alone.

Coordination properties of 2-aminocyclopentene-1-dithiocarboxylic acid to transition metal ions as studied by ab initio calculations.

The question of the(N, S) vs. (S, S) coordination mode on M x (ACDA)(2) complexes (ACDA=2-aminocyclopentene-1-dithiocarboxylic acid, M=Ni(2+), Pd(2+), Pt(2+)) was assessed through an extensive ab initio study, using the hybrid B3LYP density functional approach. The (S,S)coordination was found to be the most stable one, with an energy difference of ca. 50 kJ mol(-1) relative to the(N, S) coordination mode. Detailed analysis of the ab initio results indicates that this preference is a result of the combined effect of geometry constraints and electron distribution within the complex.

Conformational and vibrational study of platinum(II) anticancer drugs: cis-diamminedichloro-platinum(II) as a case study.

A conformational and vibrational analysis of cisplatin [cis-diamminedichloro-platinum(II)] (cDDP) is reported. Several theory methods (from Hartree-Fock to Moller-Plesset and density functional theory) combined with different all-electron basis sets are evaluated, in view of determining the best suited strategy for accurately representing this molecule. This choice is based on the best compromise between accuracy and computational requirements. Different scaling models of the cDDP vibrational modes were tested for obtaining the best scaling factors to be used in this type of inorganic systems. The structural parameters and vibrational results predicted by the calculations are compared with the corresponding experimental data, namely, x-ray structure, and Raman and inelastic neutron scattering spectra. Finally, a complete assignment of the cDDP vibrational spectra is presented.

Computationally-assisted approach to the vibrational spectra of molecular crystals: study of hydrogen-bonding and pseudo-polymorphism.

A new computationally-assisted methodology (PiMM), which accounts for the effects of intermolecular interactions in the crystal, is applied to the complete assignment of the Raman and infrared vibrational spectra of room temperature forms of crystalline caffeine, theobromine, and theophylline. The vibrational shifts due to crystal packing interactions are evaluated from ab initio calculations for a set of suitable molecular pairs, using the B3LYP/6-31G* approach. The proposed methodology provides an answer to the current demand for a reliable assignment of the vibrational spectra of these methyl-xanthines, and clarifies several misleading assignments. The most relevant intermolecular interactions in each system and their effect on the vibrational spectra are considered and discussed. Based on these results, significant insights are obtained for the structure of caffeine in the anhydrous form (stable at room temperature), for which no X-ray structure has been reported. A possible structure based on C((8))--H...N((9)) and C((1,3))--H...O intermolecular interactions is suggested.

An investigation of weak CH...O hydrogen bonds in maltose anomers by a combination of calculation and experimental solid-state NMR spectroscopy.

Two-dimensional (1)H-(13)C MAS-J-HMQC solid-state NMR spectra of the two anomeric forms of maltose at natural abundance are presented. The experimental (1)H chemical shifts of the CH and CH(2) protons are assigned using first-principles chemical shift calculations that employ a plane-wave pseudopotential approach. Further calculations show that the calculated change in the (1)H chemical shift when comparing the full crystal and an isolated molecule is a quantitative measure of intermolecular C-H...O weak hydrogen bonding. Notably, a clear correlation between a large chemical shift change (up to 2 ppm) and both a short H...O distance (<2.7 A) and a CHO bond angle greater than 130 degrees is observed, thus showing that directionality is important in C-H...O hydrogen bonding.

C-H...O hydrogen bonding in 4-phenyl-benzaldehyde: a comprehensive crystallographic, spectroscopic and computational study.

The crystal structure of 4-phenyl-benzaldehyde reveals the presence of a dimer linked by the C=O and C9-H groups of adjacent molecules. In the liquid phase, the presence of C-H...O bonded forms is revealed by both vibrational and NMR spectroscopy. A DeltaH value of -8.2 +/- 0.5 kJ mol(-1) for the dimerisation equilibrium is established from the temperature-dependent intensities of the bands assigned to the carbonyl-stretching modes. The NMR data suggest the preferential engagement of the C(2,6)-H and C(10/12)/C(11)-H groups as hydrogen bond donors, instead of the C(9)-H group. While ab initio calculations for the isolated dimers are unable to corroborate these NMR results, the radial distribution functions obtained from molecular dynamics simulations show a preference for C(2,6)-H and C(10/12)/C(11)-H...O contacts relative to the C(9)-H...O ones.

Experimental and theoretical evidence of C-H...O hydrogen bonding in liquid 4-fluorobenzaldehyde.

The presence of C-H...O hydrogen bonds in liquid 4-fluorobenzaldehyde has been studied by a combination of theoretical and spectroscopic methods. Ab initio calculations yielded bond energies and preferred bonding geometries, and the calculated spectroscopic properties have been compared with the experimental results. The presence of C-H...O hydrogen bonds in the liquid phase is strongly supported by vibrational and NMR spectroscopic data. Particular attention is paid to the spectroscopic effects related to the predicted shortening of the C-H bond engaged in the C-H...O contact. The concentration-dependent intensity in the C-H stretching region is tentatively assigned to a blue-shift effect due to C-H...O hydrogen bonding.

Spectroscopic and theoretical studies on solid 1,2-ethylenediamine dihydrochloride salt.

A structural study of [H3N(CH2)2NH3)]2+.2Cl-, the smallest element of the homologous series of the alpha,omega-diamine dihydrochlorides, was carried out by means of Raman and FTIR spectroscopy coupled to ab initio molecular orbital (MO) calculations. As a primary concern, an adequate molecular model for the representation of these solid amine salts was chosen. Thus, several models, varying in the number and position of the counterions as well as in the number of diamine units, were considered. It was found that the best molecular system (i.e., that yielding the best compromise between accuracy and computational requirements) consists of one ethylenediamine cation surrounded by six chloride ions in an arrangement based on the crystal structure reported in the literature for [H3N(CH2)2NH3)]2+.2Cl-. This conclusion will hopefully allow for a better understanding of the conformational preferences, in the solid state, of these biologically relevant linear polyamines.