Detection of the mineral constituents in human renal calculi by vibrational spectroscopic analysis combined with allied techniques Powder XRD, TGA, SEM, IR imaging and TXRF.

Detection of the mineral constituents in a batch of 310 samples of human urinary calculi (kidney stones-235 and bladder stones-75) combined with a semi-quantitative analysis has been presented on the basis of Fourier Transform based IR and Raman spectral measurements. Some of the observed characteristic IR and Raman bands have been proposed as 'Marker Bands' for the most reliable identification of the constituents. A detailed vibrational spectral analysis combined with a DFT level calculation for the functional groups in Calcium Oxalate Monohydrate (COM), Magnesium Ammonium Phosphate Hexahydrate (MAPH), Calcium Hydrogen Phosphate Dihydrate (CHPD), Penta-Calcium Hydroxy-Triphosphate (PCHT) and Uric Acid (UA) has been proposed. It has been shown that the identified mineral constituents as major or minor components can be deduced from the application of Lambert-Beer law of radiation absorption and results are in agreement with quantitative Spectral Data base. This simple method has the potential to be integrated into the management of Urolithiasis, a process of forming renal calculi in the kidney, bladder and/or urethra. Employment of powder XRD, TGA, SEM, TXRF and IR Imaging techniques has provided additional support for the proposed foolproof identification of the mineral constituents. Among the mineral constituents, Calcium Oxalate Monohydrate, Calcium Oxalate Dihydrate or their mixture account for 85% of the total number of samples; the remaining 15% and 5% samples contain Phosphate and Uric acid stones respectively.

Experimental, DFT dimeric modeling and AIM study of H-bond-mediated composite vibrational structure of Chelidonic acid.

The composite vibrational structure near 3650-3200 and 3000-2400 cm-1 in the observed IR absorption spectrum of Chelidonic acid has been explained in terms of intra- and inter-molecular -O-H∙∙∙O H-bonding attributed to monomer and dimer species computed at B3LYP/6-311++G(d,p) level. Three of the six dimer species derived out of ten monomeric components have shown both intra- and inter-molecular H-bonding. Vibrational modes of the monomer and dimer species are satisfactorily identified with the observed IR and Raman bands including frequency shifts associated with the H-bondings. The H-bond interactions in the monomer and dimer species have been characterized in terms of electron density, ρ(r), its Laplacian, ∇2ρ(r) and potential energy density at the O∙∙∙H bond critical points (BCPs) based on the Atoms in Molecules (AIM) theory. The attractive (van der Waals, H-bonds) and repulsive steric clash (SC) interactions are explained using computed reduced density gradient values from the noncovalent interaction (NCI) method. The AIM analysis confirms the presence of the intra- and inter-molecular H-bondings in the monomer/dimer species. The natural bond orbital (NBO) analysis of the natural charges and stabilization energy of the H-bonds for the dimer species further points to the stronger inter-than intra-molecular H-bonding.

Dual Fluorescence and Solvatochromic Study on 3-Acyl Coumarins.

Electronic absorption and emission spectra of 3-acetyl coumarin, 3-(bromoacetyl) coumarin and 3-(di bromoacetyl) coumarin have been recorded at room temperature in thirteen solvents with different polarities. Both ground and excited state dipole moments have been calculated for both locally excited and charge transfer transitions by using the solvatochromic method. Excited state dipole moments of all the three compounds are higher than their ground state values. DFT calculations have been profound to estimate their ground and excited state dipole moments. The estimated change in dipole moment by the application of microscopic solvent polarity parameter and bulk solvent polarity methods are in close agreement. Concentration dependent dual fluorescence has been observed in the emission spectra of all the three compounds. Graphical Abstract Dual fluorescence of 3-acetyl coumarin (I) in different solvents.

Experimental and DFT dimer modeling studies of the H-bond induced-vibration modes of l-ß-Homoserine.

The vibrational spectra for l-ß-Homoserine have been measured (IR absorption: 4000-400cm-1/Raman spectra: 4000-200cm-1). Characteristic vibrational modes of ammonium (-NH3+), carboxylate (-CO2-) and hydroxyl (-OH) groups across the 3700-1400cm-1 are all identified to have originated in inter-molecular hydrogen bonding involving these functional groups. DFT calculations at B3LYP/6-311++G(d, p) level have yielded a single neutral monomer in the gas phase. Since as a member of the amino acids which are known to possess zwitterionic structure in condensed phase, the neutral monomer of l-ß-Homoserine is optimized to a zwitterionic structure in a water medium. Consideration of two dimer structures, one dimer with -NH‧‧‧O bond and another -OH‧‧‧O bond, has given rise to vibrational modes that satisfactorily fit to all the observed absorption and Raman bands. It is found that the dimer with -OH‧‧‧O bond (binding energy, 8.896kcal/mol) is more tightly bound than the dimer with -NH‧‧‧O bond (8.363kcal/mol).

A study of hydrogen bonded vibrational spectra of (R)-(+)-Methylsuccinic acid, as aided by DFT dimer analysis.

Infrared and Raman spectral measurements in the region 4000-400cm(-1) have been carried out for (R)-(+)-Methylsuccinic acid. The vibrational band structures near 3100-3040cm(-1) in the IR and near 1650cm(-1) in the Raman spectra have indicated the presence of an inter-molecular hydrogen bonding. A DFT dimer model has been proposed that involves O-H⋯OC type of hydrogen bonding. The proposed dimer model has been derived from the three stable monomers computed at RHF/3-21G and B3LYP/6-311+G(d,p) levels of theory. A total of six dimer structures have been considered with a Boltzmann population of 38% for the most stable dimer and 62% for the remaining five dimer populations. A Boltzmann population weighted vibration spectrum has predicted bands, among others, for O-H⋯OC group that are in very good agreement with experiment. All the dimers have the same structure in that the two pairs of -O-H and -OC form a closed cyclic structure with a local center of inversion. This dimer geometry has given rise to one asymmetric mode at 1683 and one symmetric -CO mode at 1637cm(-1) corresponding to mutually exclusive an experimental IR band at 1700 and a Raman band at 1651cm(-1). Further, the bond length, H⋯O, for the most stable dimer is 1.686Å, being shorter than the sums of van der Waals radii, 2.72Å and the angle between O-H and H⋯O is almost linear (179°) suggesting that the hydrogen bonding is fairly strong.

Identification of mineral compositions in some renal calculi by FT Raman and IR spectral analysis.

We present in this paper accurate and reliable Raman and IR spectral identification of mineral constituents in nine samples of renal calculi (kidney stones) removed from patients suffering from nephrolithiasis. The identified mineral components include Calcium Oxalate Monohydrate (COM, whewellite), Calcium Oxalate Dihydrate (COD, weddellite), Magnesium Ammonium Phosphate Hexahydrate (MAPH, struvite), Calcium Hydrogen Phosphate Dihydrate (CHPD, brushite), Pentacalcium Hydroxy Triphosphate (PCHT, hydroxyapatite) and Uric Acid (UA). The identification is based on a satisfactory assignment of all the observed IR and Raman bands (3500-400c m(-1)) to chemical functional groups of mineral components in the samples, aided by spectral analysis of pure materials of COM, MAPH, CHPD and UA. It is found that the eight samples are composed of COM as the common component, the other mineral species as common components are: MAPH in five samples, PCHT in three samples, COD in three samples, UA in three samples and CHPD in two samples. One sample is wholly composed of UA as a single component; this inference is supported by the good agreement between ab initio density functional theoretical spectra and experimental spectral measurements of both sample and pure material. A combined application of Raman and IR techniques has shown that, where the IR is ambiguous, the Raman analysis can differentiate COD from COM and PCHT from MAPH.

(R)-(-)-2-Pyrrolidinemethanol: A combined experimental and DFT vibrational analysis of monomers, dimers and hydrogen bonding.

Experimental IR and solution phase spectra of (R)-(-)-2-Pyrrolidinemethanol showing evidence of hydrogen bonding have been interpreted by computing vibrational modes of monomers and dimers with the molecular species due to intra- and inter-molecular hydrogen bonding, at B3LYP/6-311+G(d,p) level density functional theoretical calculations. Computed vibrational frequencies of Boltzmann population-weighted dimers for stretching and bending of O-H and N-H modes associated with the inter-molecular N-H⋯O and O-H⋯O hydrogen bonding are in good agreement with the measured IR absorption, Raman and solution-phase IR values near 3289 cm(-1), 3450 cm(-1) and 1400-1300 cm(-1). Further, the H⋯O length is shorter in O-H⋯O than in N-H⋯O by ∼10% suggesting that O-H⋯O is a stronger bond. While the solution-phase IR spectral features suggest strong inter-molecular associations, it is short of demonstrating which type of bonding is dominant factor. We conclude that the measured IR, Raman and solution-phase IR spectral features indicate the presence of both types of hydrogen bonds.

1-(3,4-Di-fluoro-benz-yl)-4-(4-methyl-phenyl-sulfon-yl)piperazine.

In the title compound, C18H20F2N2O2S, the central piperazine ring adopts a chair conformation. The dihedral angle between the two benzene rings is 40.20°, whereas those between the piperazine ring (considering the best fit plane through all the non-H atoms) and the sulfonyl-bound benzene and di-fluoro-benzene rings are 74.96 and 86.16°, respectively. In the crystal, mol-ecules are stacked along the a axis through weak C-H⋯O and C-H⋯F inter-actions.

An unknown solvate of 1-(2,4-di-chloro-benz-yl)-4-[(4-methyl-phen-yl)sulfon-yl]piperazine.

In the title compound, C18H20Cl2N2O2S, the piperazine ring adopts a chair conformation. The dihedral angle between the sulfonyl-bound benzene ring and the best-fit plane through the six non-H atoms of the piperazine ring is 72.22 (12)°; those between the di-chloro-benzene ring and the sulfonyl and piperazine rings are 2.44 (13) and 74.16 (2)°, respectively. In the crystal, mol-ecules are connected through weak C-H⋯O inter-actions into a hexa-meric unit generating a R 6 (6)(60) motif in the ab plane. The mol-ecules are also connected into C(4) chains through weak C-H⋯N inter-actions. The solvent used to grow the crystal was a mixture of di-chloro-methane and methanol, but the resulting electron density was uninter-pretable. The solvent contribution to the scattering was removed with the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148-155]. The formula mass and unit-cell characteristics do not take into account the disordered solvent.

(2,3-Difluoro-phen-yl)(4-tosyl-piperazin-1-yl)methanone.

In the title compound, C(18)H(18)F(2)N(2)O(3)S, the piperazine ring adopts a chair conformation. The dihedral angle between the sulfonyl-bound benzene ring and the best fit plane throught the six non-H atoms of the piperazine ring is 69.4 (2)°, while those between the fluoro-benzene and sulfonyl rings and the fluoro-benzene and piperazine rings are 30.97 (2) and 75.98 (2)°, respectively. In the crystal, mol-ecules are connected to form a tetra-meric unit through C-H⋯O hydrogen bonds. The structure is further stabilized by weak inter-molecular C-H⋯F inter-actions, generating C(8) and C(7) chains running along [100].

1-Tosyl-4-[2-(trifluoro-meth-yl)benz-yl]piperazine.

In the crystal structure of the title compound, C(19)H(21)F(3)N(2)O(2)S, the piperazine ring adopts a chair conformation. The dihedral angles between the mean plane of the piperazine ring and the tosyl and trifluoro-methyl-phenyl rings are 74.52 (3) and 68.30 (2)°, respectively. The sulfonamide N atom deviates from the plane defined by the three attached atoms by 0.327 (1) Å. The crystal structure is stabilized by weak C-H⋯π inter-actions.

N-[(2-Chloro-phen-yl)sulfon-yl]-2-meth-oxy-benzamide.

The title compound, C14H12ClNO4S, crystallizes with two mol-ecules in the asymmetric unit. The dihedral angles between the benzene rings are 89.68 (1) (mol-ecule 1) and 82.9 (1)° (mol-ecule 2). In each mol-ecule, intra-molecular N-H⋯O hydrogen bonds between the amide H atom and the meth-oxy O atom generate S(6) loops. In the crystal, mol-ecule 2 is linked into inversion dimers through pairs of C-H⋯O inter-actions, forming an R 2 (2)(8) ring motif. Mol-ecules 1 and 2 are further linked along the b-axis direction through C-H⋯π inter-actions. The crystal structure is further stabilized by several π-π stacking inter-actions [centroid-centroid separations = 3.7793 (1), 3.6697 (1) and 3.6958 (1) Å], thus generating a three-dimensional architecture.

Vibration and DFT analysis of 2-methyl-3-nitrophenyl isocyanate and 4-methyl-2-nitrophenyl isocyanate.

Vibrational spectra of 2-methyl-3-nitrophenyl isocyanate and 4-methyl-2-nitrophenyl isocyanate, in the spectral region 4000-100 cm(-1), have been measured and assigned. Conformational and harmonic frequency analyses have been performed at B3LYP/6-311G(∗) level of calculations. The two stable conformers, cis and trans, have been computed for each of the molecules. It has been determined that the trans conformer has lower energy than the cis by 3.954 kJ/mol for 2-methyl-3-nitrophenyl isocyanate; whereas the cis conformer has lower energy than the trans by 10.230 kJ/mol for 4-methyl-2-nitrophenyl isocyanate. The vibration structure of 2-methyl-3-nitrophenyl isocyanate conforms to the combined behavior of its both conformers from which the deviation is shown by the structure of 4-methyl-2-nitrophenyl isocyanate which follows only the trans conformer. The occurrence of symmetric mode of the methyl group at higher frequency near 2944-20 cm(-1) is attributed to the phenyl ring strain caused by the substituents. As for the other stretching and bending modes, mutually exclusive pattern appears to work for the molecules: The nitro group's non-coplanarity with the phenyl ring is more evident in 4-methyl-2-nitrophenyl isocyanate where the asymmetric mode was assigned to the band at 1569cm(-1), whereas the symmetric mode at lower frequency 1339cm(-1). Occasional doublet appearance of the strong asymmetric absorption near 2282cm(-1) due to isocyanate moiety has been observed in the present study and is assumed to arise from the torsional vibration motion of the moiety rendered by the small energy gap between the conformers of 2-methyl-3-nitrophenyl isocyanate.

2-Methoxyphenyl isocyanate and 2-Methoxyphenyl isothiocyanate: conformers, vibration structure and multiplet Fermi resonance.

IR and Raman spectral measurements in the region 3500-400/50 cm(-1) have been made for the liquid samples of 2-Methoxyphenyl isocyanate and 2-Methoxyphenyl isothiocyanate. A complete assignment of the measured bands has been proposed as aided by conformational and vibration analyses at B3LYP/6-311++G** level of calculations. Three conformers for 2-Methoxyphenyl isocyanate and two for 2-Methoxyphenyl isothiocyanate have been determined. The tilt of the isocyanate (NCO) and isothiocyanate (NCS) moieties with respect to phenyl ring are in broad agreement with their parents. Stretching mode frequencies of methyl group (-OCH(3)) in 2-Methoxyphenyl isocyanate have been lowered in the 2900-2800 cm(-1); deformation asymmetric modes are IR strong and symmetric one Raman strong. In 2-Methoxyphenyl isothiocyanate, a similar pattern is true for stretching modes but deformation asymmetric modes are IR strong and symmetric mode has not been observed. Multiplet absorption band system near 2200 cm(-1) in 2-Methoxyphenyl isocyanate has been interpreted to be caused by Fermi resonance. A similar pattern in absorption near 2100 cm(-1) in 2-Methoxyphenyl isothiocyanate but more complex Raman band pattern has also been explained through Fermi resonance from heuristic stand-point. Many Raman modes in 1300-1100 cm(-1) are intensified apparently owing to isothiocyanate than isocyanate moiety. Phenyl ring breathing mode is shifted to 1040 cm(-1) as strong Raman; the symmetric stretching mode of O-CH(3) near 1023 cm(-1) as strong absorption.

Effect of nitro groups on the photo physical properties of benzimidazolone: a solvatochromic study.

Electronic absorption and fluorescence spectra of mono, di, and tri-nitro benzimidazolones are measured at room temperature (298 K) in nine solvents with different polarities and the observed shifts are compared with benzimidazolone. Ground and excited state electric dipole moments are determined using the solvatochromic method based on the bulk solvent properties, F(1)(ε, n) and F(2)(ε, n). A reasonable agreement is observed between the experimental and ab initio dipole moments. Change in dipole moment is also determined using the solvatochromic method based on the microscopic solvent polarity parameter, (E(T)(N)), which considers the polarization changes due to hydrogen bonding in different solvents. It has been observed that the correlation of the solvatochromic Stokes shifts with the parameter (E(T)(N)), is superior to that derived using bulk solvent polarity functions for all the benzimidazolones reported in the present study. Calculated difference between excited state and ground state dipole moments seems to be a good measure of the effect of nitro group when correlated with (E(T)(N)).

2-Chloro- and 2-bromo-3-pyridinecarboxaldehydes: structures, rotamers, fermi resonance and vibration modes.

FT-Infrared (4000-400 cm(-1)) and NIR-FT-Raman (4000-50 cm(-1)) spectral measurements have been made for 2-chloro- and 2-bromo-3-pyridinecarboxaldehydes. A DFT vibration analysis at B3LYP/6-311++G (d,p) level, valence force-fields and vibrational mode calculations have been performed. Aided by very good agreement between observed and computed vibration spectra, a complete assignment of fundamental vibration modes to the observed absorptions and Raman bands has been proposed. Orientations of the aldehydic group have produced two oblate asymmetric rotamers for each molecule, ON-trans and ON-cis: the ON-trans rotamer being more stable than cis by 3.42 kcal mol(-1) for 2-chloro-3-pyridinecarboxaldehyde and 3.68 kcal mol(-1) for 2-bromo-3-pyridinecarboxaldehyde. High potential energy barrier ca 14 kcal/mol, induced by steric hindrance, restricts rotamers' population to ON-trans only. It is observed that, in the presence of bromine, C-H stretching modes are pronounced; a missing characteristic ring mode in chlorine's presence shows at 1557 cm(-1); the characteristic ring mode at 1051 cm(-1) is diminished; a mixed mode near 707 cm(-1) is enhanced. Further, an observed doublet near 1696-1666 cm(-1) in both IR and Raman spectra is explained on the basis of Fermi resonance between aldehydic carbonyl stretching at 1696 cm(-1) and a combination mode of ring stretch near 1059 cm(-1) and deformation vibration, 625 cm(-1). A strong Raman aldehydic torsional mode at 62 cm(-1) is interpreted to correspond to the dominant ON-trans over cis rotamers population.

Hydrogen bond, dimerization and vibrational modes in 2-chloro-3-hydroxybenzaldehyde and 3-chloro-4-hydroxybenzaldehyde from vibrational and ab initio studies.

Ab initio conformers and dimers have been computed at RHF and B3LYP/6-31G* levels for isomers 2-chloro-3-hydroxybenzaldehyde and 3-chloro-4-hydroxybenzaldehyde to explain the observed infrared absorption and Raman vibrational spectral features in the region 3500-50 cm(-1). The position of the chlorine in ortho position with respect to aldehyde group in 2-chloro-3-hydroxybenzaldehyde yields four distinct conformers; whereas the chlorine in meta position in 3-chloro-4-hydroxybenzaldehyde yields effectively only three conformers. Major spectral features as strong absorptions near 3160-80 cm(-1), down-shifting of the aldehydic carbonyl stretching mode and up-shifting of hydroxyl group's in-plane bending mode are explained using ab initio evidence of O-H⋯O bond-aided dimerization between the most stable conformers of each molecule. Absorption width of about 700 cm(-1) (∼8.28 kJ/mol) of O-H stretching modes suggests a strong hydrogen bonding with the ab initio bond lengths, O-H⋯O in the range of 2.873-2.832 Å. A strong Raman mode near 110-85 cm(-1) in each molecule is interpreted to be coupled vibrations of pseudo-dimeric trans and cis structures.

Ab initio/DFT electronic structure calculations, spectroscopic studies and normal coordinate analysis of 2-chloro-5-bromopyridine.

FT-IR (4000-400 cm(-1)) and FT-Raman (3500-50 cm(-1)) spectral measurements of solid sample of 2-chloro-5-bromopyridine have been done. Ab initio and DFT calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, depolarization ratios, IR intensities, Raman activities and atomic displacements. Furthermore, force field calculations have been performed by normal coordinate analysis. A complete assignment of the observed spectra, based on spectral correlations, electronic structure calculations and normal coordinate analysis, has been proposed. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The SQM method, which implies multiple scaling of the DFT force fields, has been shown superior to the uniform scaling approach. The energy and oscillator strength calculated by Time-dependent DFT results are in good agreement with the experimental results.

Vibrational and ab initio studies of 3-acetyl-6-bromocoumarin and 3-acetyl-6-methylcoumarin.

Infrared absorption and Raman spectra (3500-50 cm(-1)) of 3-acetyl-6-bromocoumarin and 3-acetyl-6-methylcoumarin have been measured and interpreted, aided by electronic structure calculations at RHF and B3LYP using 6-31(d, p) basis set. It has been determined that the rotation of the acetyl group with respect to the coumarin ring results in three conformers--two trans and one cis--for each molecule, with one trans conformer being the most stable in both cases. There are significant changes in the vibrational structure as characterized by positions and intensities of certain modes in going from 3-acetyl-6-bromocoumarin to 3-acetyl-6-methylcoumarin. The carbonyl stretching mode of the pyrone ring is stable in both molecules whereas the same mode in acetyl groups is not. Ring stretching vibrations are coupled to C-H in-plane bending vibrations. Down-shifting of frequencies of methyl vibrations in acetyl group occurs vis-à-vis methyl vibrations in 3-acetyl-6-methylcoumarin. A strong Raman band at 126 cm(-1) in both molecules is structure-independent non-genuine mode, correlated to lattice vibrations in the solid phase.

Vibrational spectra, normal modes, ab initio and DFT calculations for 6-Chloro- and 7-Chloro-4-bromomethylcoumarins.

Vibration spectral measurements - Infrared (4000-400 cm(-1)) and Raman (3500-50 cm(-1)) spectra - have been made for the solid samples of 6-Chloro- and 7-Chloro-4-bromomethylcoumarins. Ground electronic state energies, equilibrium geometries, harmonic vibrational spectra and normal modes have been computed using ab initio - RHF/6-31G* - and DFT - B3LYP/6-31G* levels of theory. The optimization yielded three structures for each molecule, with one being a transition state structure. Of the remaining two conformers, one belongs to C(s) symmetry and the other belongs to C(1), the latter being the most stable one. The optimized dihedral angle for -CH(2)Br group is 111 degrees in agreement with X-ray diffraction results reported for the similar molecular systems. Assignment of all the observed spectral bands has been proposed. The absorptions show band pattern revealing isomer characteristics and vibrational coupling in varying degrees; the Raman spectra show structural changes associated with the rings as well as lattice modes.