Surface-enhanced resonance Raman scattering and density functional calculations of hemicyanine adsorbed on colloidal silver surface

Resonance Raman (RR) and surface-enhanced resonance Raman scattering (SERRS) of 4'-(N,N'-dimethylaminostyryl)-4-propylpyridinium bromide (hemicyanine, HC dye) in acetonitrile solution and on a colloidal silver surface have been investigated. The structure of the dye in the ground (S0) and excited (S1) electronic states was optimized using density functional calculations along with the B3LYP and the configuration interaction with the singlet excitation (CIS) methods, respectively, using the 6-31G basis set. The vibrational frequencies of the molecule were computed at the optimized geometry and compared with the observed Raman bands. A complete normal-mode analysis has been carried out because it is essential for the accurate assignment of the vibrational spectra. From the observed enhancement along various in-plane and out-of-plane vibrations in the SERRS spectrum and from theoretical calculations, it has been inferred that the interaction with the silver surface occurs via the nitrogen lone pair of the pyridyl or the dimethylamino group of the molecule with a tilted orientation. The observed red-shifts in the SERRS spectrum along various vibrations indicate strong interaction (chemisorption) of the HC dye with the silver surface. This is also supported by the presence of a Ag-N stretching vibration at 241 cm(-1). The effect of the dye concentration on the orientation of the molecule is also discussed.     

Synthesis,Crystal and Molecular Structure of Mono- and Diaquadi(acetato-O)-Bis(2,4′-Bipyridyl) Copper(II)

The title compound has been synthesized and characterized by elemental analysis and conductivity studies. The crystal and molecular structure has been determined. There are two different types of molecules in the crystal: mono- and diaquadi(acetato-O)-bis(2,4'-bipyridyl) copper (II). Both copper atoms occupy special positions. The copper atoms show almost ideal square pyramidal (4 + 1) and square bipyramidal (4 + 2) coordination. Due to the Jahn-Teller effect, the axial Cu-O(water) bond distances are longer than respective equatorial Cu-O(acetate) bond distances. The bond valences of the copper were computed. An intramolecular strong hydrogen bond linking O(water) and O(acetate) atoms exists in the molecule. The differences of geometrical environment for copper in mono- and diaquadi(acetato-O)-bis(2,4'-bipyridyl) copper(II) are imposed by strong intermolecular hydrogen bonds creating a linear infinite chain structure along crystallographic x axis. Also weak intramolecular hydrogen bonds are present in the molecule.     

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of p-amino acetanilide

The infrared absorption, Raman spectra and SERS spectra of p-amino acetanilide have been analyzed with the aid of density functional theory calculations at B3LYP/6-311G(d,p) level. The electric dipole moment (mu) and the first hyperpolarizability (beta) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the synthesized molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Computed geometries reveal that the PAA molecule is planar, while secondary amide group is twisted with respect to the phenyl ring is found, upon hydrogen bonding. The hyperconjugation of the C=O group with adjacent C-C bond and donor-acceptor interaction associated with the secondary amide have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation and hyperconjugation. The existence of intramolecular C=O...H hydrogen bonded have been investigated by means of the natural bonding orbital (NBO) analysis. The influence of the decrease of N-H and C=O bond orders and increase of C-N bond orders due to donor-acceptor interaction has been identified in the vibrational spectra. The SERS spectral analysis reveals that the large enhancement of in-plane bending, out of plane bending and ring breathing modes in the surface-enhanced Raman scattering spectrum indicates that the molecule is adsorbed on the silver surface in a 'atleast vertical' configuration, with the ring perpendicular to the silver surface.     

Charge transfer interaction and terahertz studies of a nonlinear optical material L-glutamine picrate: A DFT study

Charge transfer interaction, vibrational spectra, and DFT computation of l-glutamine picrate has been analyzed. The equilibrium geometry, bonding features, and harmonic vibrational wavenumbers have been investigated with the help of B3LYP density functional theory method. The natural bond orbital analysis confirms the occurrence of strong intramolecular hydrogen bonding in the molecule. Terahertz time-domain spectroscopy was used to detect the absorption spectra in the frequency range from 0.025 to 2.8 THz. The vibrational modes found in molecular crystalline materials should be described as phonon modes with strong coupling to the intramolecular vibrations.     

Inter- and intramolecular hydrogen bonding in phenol derivatives: a model system for poly-L-tyrosine

The ultrafast dynamics of solutions of phenol and two phenol derivatives--hydroquinone (1,4-benzenediol) and pyrocatechol (1,2-benzenediol)--have been studied with Optically Heterodyne-Detected Optical Kerr-Effect (OHD-OKE) spectroscopy. The solvents, methanol and acetonitrile, were selected to provide strong and weak solvent-solute hydrogen-bonding interactions, respectively, while pyrocatechol features an intramolecular hydrogen bond. Together these provide a series of model systems for polypeptides such as polytyrosine, which facilitate the direct study of inter- and intramolecular hydrogen bonding. A broad contribution to the Raman spectral density of the methanol solutions at frequencies between 150 and 300 cm(-1) has been observed that is absent in acetonitrile. This contribution has been assigned to solvent-solute hydrogen-bond stretching vibrations. The OHD-OKE response of poly-L-tyrosine has been measured and was found to contain a similar contribution. Density functional theory geometry optimizations and normal mode calculations have been performed using the B3LYP hybrid functional and 6-311++G** basis set. These have yielded a complete assignment of the low-frequency Raman and far-infrared spectra of pyrocatechol for the first time, which has provided information on the nature of the intramolecular hydrogen bond of pyrocatechol.     

DFT computations,vibrational spectra,monomer, dimer,NBO and NMR analyses of antifungal agent: 3,5-Dibromosalicylic acid

The experimental and theoretical study on the structures and vibrations of 3,5-dibromosalicylic acid (DBSA) are presented. The FT-IR and FT-Raman of the title compound have been recorded. The molecular structures, vibrational wavenumbers, infrared intensities, Raman activities were calculated. The energies of DBSA are obtained for all the eight conformers from density functional theory with 6-311++G(d,p) basis set calculations. From the computational results, C1 or C5 forms are identified as the most stable conformers of DBSA. The spectroscopic and theoretical results are compared with the corresponding properties for DBSA monomer and dimer of C1 (or C5) conformer. Intermolecular hydrogen bonds are discussed in dimer structure of the molecule. NBO analysis is useful to understand the intramolecular hyperconjugative interaction between lone pair O9 and C7O8. The calculated HOMO–LUMO energies reveal charge transfer occurs within the molecule. The polarizability, first hyperpolarizability, anisotropy polarizability invariant has been computed using quantum chemical calculations. The isotopic chemical shift computed by ¹H and ¹³C nuclear magnetic resonance (NMR) chemical shifts of the DBSA molecule, calculated using the gauge invariant atomic orbital (GIAO) method, also shows good agreement with experimental observations.     

Shape of 4S- and 4R-hydroxyproline in gas phase

The alpha-amino acids 4(S)-hydroxyproline and 4(R)-hydroxyproline have been studied under isolation conditions in gas phase using laser-ablation molecular-beam Fourier transform microwave spectroscopy. Two conformers of each molecule have been detected in the jet-cooled rotational spectrum. The most stable conformer in both molecules exhibits an intramolecular N...H-O hydrogen bond (configuration 1) between the hydrogen atom of the carboxylic group and the nitrogen atom. The second conformer is characterized by an intramolecular N-H...O=C hydrogen bond (configuration 2). The conformers of 4(R)-hydroxyproline adopt a C(gamma)-exo puckering, while those of 4(S)-hydroxyproline present a C(gamma)-endo ring conformation. These ring conformations, which show the same propensity observed in collagen-like peptides, are stabilized by additional intramolecular hydrogen bonds involving the 4-hydroxyl group, with the exception of the most stable form of 4(S)-hydroxyproline for which a n-pi interaction between the oxygen atom of the 4-hydroxyl group and the carboxyl group carbon seems to be established. A gauche effect could be also contributing to stabilize the observed conformers.     

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 ?. 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.     

A Mixed Quantum-Classical Approach for Computing Effects of Intramolecular Motion on the Low-Barrier Hydrogen Bond

The fractionation factor is defined as the equilibrium constant for the reaction: R – H + DOH R – D + HOH. Of interest are values of fractionation factors for reactions where reactants and/or products form intramolecular low-barrier hydrogen bonds. Experimentally measured isotopic fractionation factors are usually interpreted via a one-dimensional potential energy surface along the intrinsic proton hydrogen bond coordinate. Such a one-dimensional picture cannot be completely correct. Intramolecular motions, such as vibrations and librations, can modulate the underlying potential energy surface along the hydrogen bond coordinate and thus affect the isotopic fractionation factor. We have recently generated a picture of the motion of the proton in a low-barrier hydrogen bond as taking place in an effective single-dimensional potential, which we term the potential of mean force (PMF). In this paper, we compute the PMF for a molecule with an intramolecular hydrogen bond in order to quantify the effect of intramolecular motions on the fractionation factor. The PMF and isotopic fractionation factor are computed with a combination of high-level density functional theory and molecular dynamics simulations.     

Intramolecular hydrogen bonding in 1-nitro-5,10-dihydrophenazine derivatives

The formation of free radicals only for derivatives with a nitro group in the 1 position was observed in the oxidation of a number of 5-substituted 5,10-dihydrophenazines with lead dioxide. A long-wave absorption band was observed in the electronic spectra of the derivatives with a nitro group in the 1 position. The assumption of the formation of an intramolecular hydrogen bond in dihydrophenazines with a nitro group in the 1 position was confirmed by quantum-chemical modeling of the three structures of the 1,3-dinitro-5-phenyl-5,10-dihydrophenazine molecule. By comparison of the integral intensities of the bands of the stretching vibrations of the N-H bond in 5-substituted dihydrophenazines it was concluded that this bond is depolarized in derivatives with an intramolecular hydrogen bond.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No, 2, pp, 263–265, February, 1978.     

Theoretical estimates of the IR spectrum of formamide intercalated into kaolinite

Calculations at PM3 and PBE/6‐31G levels of part of the IR spectrum of the formamide‐kaolinite intercalatation compound based on a 110‐atom cluster of kaolinite with one formamide molecule are reported. Frequencies and intensities for the formamide vibrations and stretchings of four cluster hydroxyls were calculated through partial hessian matrices and polar tensors obtained by numerical differentiation of energy gradients and dipole moment. The formamide molecule attaches to the kaolinite inner surfaces in multiple conformations with its CN bond vector parallel to the surfaces. Hydrogen bonds are formed between the formamide hydrogen atoms (both from NH₂ or CH groups) and the siloxane surface and between the formamide oxygen and nitrogen atoms and the aluminol hydroxyls. The general features of the experimental assignment of the spectrum are confirmed, but the observed splitting of formamide bands is attributed to vibrations from differently attached molecules. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Interaction of glycine with isolated hydroxyl groups at the silica surface: first principles B3LYP periodic simulation

The adsorption of a glycine molecule on a model silica surface terminated by an isolated hydroxyl group has been studied ab initio using a double-zeta polarized Gaussian basis set, the hybrid B3LYP functional, and a full periodic treatment of the silica surface/glycine system. The hydroxylated silica surface has been simulated using either a 2D slab or a single polymer strand cut out from the (001) surface of an all-silica edingtonite. A number of B3LYP-optimized structures have been found by docking glycine on the silica surface exploiting all possible hydrogen bond patterns. Whereas glycine is generally adsorbed in its neutral form, two structures show glycine adsorbed as a zwitterion, the surface playing the role of a "solid solvent" whereas intrastrand hydrogen bond cooperativity stabilizes the zwitterions. The adsorbed zwitterionic structures are no longer formed at a lower glycine coverage as simulated by enlarging the unit cell so as to break intrastrand hydrogen bonds, showing the importance of H-bond cooperativity in stabilizing the zwitterionic forms. Each structure has been characterized by computing its harmonic vibrational spectrum at the Gamma point, which also allowed us to calculate the free energy of adsorption. The experimental infrared features of chemical-vapor-deposited glycine on a silica surface are in agreement with those computed for glycine adsorbed in its neutral form and engaging three hydrogen bonds with the surface silanols, two of them involving the C=O bond and one originating from the glycine OH group. The NH(2) group plays only a minor role as a weak hydrogen bond donor.     

Effect of the resonance of molecular vibrations on the ir spectra of hydrogen bonds

The effects are considered of the vibrations occurring with the group of atoms peripheral towards the hydrogen bond on the IR spectrum of the model hydrogen bond. It. is shown that the resonance of the v_OHv_CH stretching vibrations in a hydrogen bonded molecule result in the division of the v_OH band into two other bands having different polarizations. The resonance interaction leads to redistribution of the intensity and perturbs the regular Franck—Condon type envelope of the spectrum.     

Influence of Hydrogen Bonding and Polarity on the Spectral Properties of 4-Aminophthalimide Clusters Formed with Triethylamine and Dimethyl Sulfoxide in Solution

The time-dependent density functional theory (TDDFT) method has been carried out to study the influences of hydrogen bonding and solvent polarity on the spectral properties of 4-aminophthalimide (4AP) clusters formed with hydrogen-accepting solvents triethylamine (TEA) and dimethyl sulfoxide (DMSO). The ground- and S₁-state geometry structure optimizations, hydrogen bond energies, absorption and emission spectra for both the 4AP monomer and its two triply hydrogen-bonded clusters 4AP + (TEA)₃ and 4AP + (DMSO)₃ have been calculated using DFT and TDDFT methods respectively with the hybrid exchange correlation functional PBE1PBE and split-valence basis set 6-311++G(d,p). It has been demonstrated that the two hydrogen bonds I and II formed with the amine group of 4AP are significantly strengthened while the hydrogen bond III formed with the imide group is slightly weakened due to the intramolecular charge transfer from the amine group to the two carbonyl groups of the 4AP molecule upon photoexcitation. In addition, the hydrogen bonds formed by 4AP with DMSO are stronger than those formed with TEA, which together with its strong polarity, should be the main reasons for the more redshifts of both the absorption and the fluorescence spectra of 4AP in solvent DMSO than those in TEA.     

Vibrational assignment, structure and intramolecular hydrogen bond study of 3-amino-1-phenyl-2-buten-1-one

Fourier transform infrared and Fourier transform Raman spectra of 3-amino-1-phenyl-2-buten-1-one and its deuterated analogue were recorded in the regions 400-4,000 and 150-4,000 cm(-1), respectively. Furthermore, the molecular structure and vibrational frequencies of title compound were investigated by a series of density functional theoretical, DFT, and ab initio calculations at the post-Hartree-Fock (MP2) level. Although, the calculated frequencies are generally in agreement with the observed spectra but the DFT results are in much better quantitative agreement with the observed spectra than the MP2 results. The observed wavenumbers were analyzed and assigned to different normal modes of vibration of the molecule. The calculated geometrical parameters show a strong intramolecular hydrogen bond with a N...O distance of 2.621-2.668 A. This bond length is shorter than that of its parent, 4-amino-3-penten-2-one (with two methyl groups in the beta-position), which is in agreement with spectroscopic results. The topological properties of the electron density contributions for intramolecular hydrogen bond in 3-amino-1-phenyl-2-buten-1-one and 4-amino-3-penten-2-one have been analyzed in term of the Bader theory of atoms in molecules (AIM). These results also support the stronger hydrogen bond in the title compound with respect to the parent molecule.     

Crystal structure of 3-diethylaminomethyl-2,2′-biphenol

Crystals of 3-diethylaminomethyl-2,2′-biphenol were examined using X-ray diffraction and FT-IR spectroscopy. Their space group is P2₁/c with a=7.305(1), b=13.816(2), c=29.232(4) Å, β=92.411(3)° and Z=8. The unit cell contains two symmetry-independent zwitterions. The hydrogen atom of the protonated diethylaminomethyl group is linked to the negatively charged phenolate oxygen atom, which in turn is linked to the hydroxyl group by a short hydrogen bond (molecule a: NO=2.604(3), OO=2.512(3) Å; molecule b: NO=2.593(4), OO=2.489(4) Å). The OHO⁻H⁺N bifurcated intramolecular hydrogen bonds are crystallographically asymmetric. The IR spectrum of the crystals confirms very well the results obtained by the X-ray study. Instead of continuous absorption, only broad bands are found indicating relatively low proton polarisability in the two types of intramolecular hydrogen bonds.     

Surface enhanced Raman scattering of ammonia

A surface enhanced Raman scattering (SERS) spectrum of 0.5 M NH₃ in 4.0 M KCl has been observed on a silver electrode. An approximate enhancement factor of 3 × 10⁵ is calculated, and additional evidence for the enhanced nature of the spectrum is provided by the observation that totally symmetric vibrations are depolarized and by the strong potential dependence of the intensity of surface lines. Assignments have been given to the SERS lines with the low-frequency lines assigned to a AgCl and AgN stretch. The positive shift of the maximum of the intensity versus voltage curve with a lower laser excitation frequency is taken as evidence for the occurrence of a charge transfer process from ammonia to the silver electrode. The fact that the SERS spectrum of NH₃ on Ag can only be observed at large electrolyte concentrations is attributed to the breaking of hydrogen bonding at the electrode-solution interface.     

Molecular Insight into Long‐Wavelength Fluorogenic Dye Design: Hydrogen Bond Induces Activation of a Dormant Acceptor

The detection of chemical or biological analytes in response to molecular changes relies increasingly on fluorescence methods. Therefore, there is a substantial need for the development of improved fluorogenic dyes. In this study, we demonstrated how an intramolecular hydrogen bond activates a dormant acceptor through a charge induction between phenolic hydrogen and a heteroaryl nitrogen moiety. As a result, a new fluorochrome is produced, and the molecule exhibits a strong fluorescent emission. When the strength of the hydrogen bonding was increased by conformational locking, the obtained dye emitted at longer wavelengths and fluoresced under physiological conditions. The dye was implemented in a turn‐ON system responsive to hydrogen peroxide. The molecular insight provided by this study should assist in the design of fluorescent dyes that are suitable for in vitro and in vivo applications.     

Structure of Isolated 1,4-Butanediol: Combination of MP2 Calculations, NBO Analysis, and Matrix-Isolation Infrared Spectroscopy

Theoretical calculations at the MP2 level, NBO and AIM analysis, and matrix-isolation infrared spectroscopy have been used to investigate the structure of the isolated molecule of 1,4-butanediol (1,4-BDO). Sixty-five structures were found to be minima on the potential energy surface, and the three most stable forms are characterized by a folded backbone conformation leading to the formation of an intramolecular H-bond. To better characterize the intramolecular interactions and particularly the hydrogen bonds, natural bond orbital analysis (NBO) was performed for the four most stable conformers, and was further complemented with an atoms-in-molecules (AIM) topological analysis. Infrared spectra of 1,4-BDO isolated in low-temperature argon and xenon matrixes show a good agreement with a population-weighted mean theoretical spectrum, and the spectral features of the conformers expected to be trapped in the matrixes were observed experimentally. Annealing the xenon matrix from 20 to 60 K resulted in significant spectral changes, which were interpreted based on the barriers to intramolecular rotation. An estimation of the intramolecular hydrogen bond energy was carried out following three different methodologies.     

A microwave spectroscopic and quantum chemical study of 3-butyne-1-selenol (HSeCH2CH2C[triple bond]CH)

The microwave spectrum of 3-butyne-1-selenol has been studied by means of Stark-modulation microwave spectroscopy and quantum chemical calculations employing the B3LYP/aug-cc-pVTZ and MP2/6-311++G(3df,3pd) methods. Rotational transitions attributable to the H80SeCH2CH2C[triple bond]CH and H78SeCH2CH2C[triple bond]CH isotopologues of two conformers of this molecule were assigned. One of these conformers possesses an antiperiplanar arrangement for the atoms Se-C-C-C, while the other is synclinal and seems to be stabilized by the formation of a weak intramolecular hydrogen bond between the hydrogen atom of the selenol group and the pi electrons of the CC triple bond. The energy difference between these conformers was determined to be 0.2(5) kJ/mol by relative intensity measurements, and the hydrogen-bonded form was slightly lower in energy.