Hydrogen bond lifetimes and energetics for solute/solvent complexes studied with 2D-IR vibrational echo spectroscopy

Weak pi hydrogen-bonded solute/solvent complexes are studied with ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy, temperature-dependent IR absorption spectroscopy, and density functional theory calculations. Eight solute/solvent complexes composed of a number of phenol derivatives and various benzene derivatives are investigated. The complexes are formed between the phenol derivative (solute) in a mixed solvent of the benzene derivative and CCl4. The time dependence of the 2D-IR vibrational echo spectra of the phenol hydroxyl stretch is used to directly determine the dissociation and formation rates of the hydrogen-bonded complexes. The dissociation rates of the weak hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. The results are discussed in terms of transition state theory.     

Solute-solvent complex kinetics and thermodynamics probed by 2D-IR vibrational echo chemical exchange spectroscopy

The formation and dissociation kinetics of a series of triethylsilanol/solvent weakly hydrogen bonding complexes with enthalpies of formation ranging from -1.4 to -3.3 kcal/mol are measured with ultrafast two-dimensional infrared (2D IR) chemical exchange spectroscopy in liquid solutions at room temperature. The correlation between the complex enthalpies of formation and dissociation rate constants can be expressed with an equation similar to the Arrhenius equation. The experimental results are in accord with previous observations on eight phenol/solvent complexes with enthalpies of formation from -0.6 to -2.5 kcal/mol. It was found that the inverse of the solute-solvent complex dissociation rate constant is linearly related to exp(-DeltaH0/RT) where DeltaH0 is the complex enthalpy of formation. It is shown here, that the triethylsilanol-solvent complexes obey the same relationship with the identical proportionality constant, that is, all 13 points, five silanol complexes and eight phenol complexes, fall on the same line. In addition, features of 2D IR chemical exchange spectra at long reaction times (spectral diffusion complete) are explicated using the triethylsilanol systems. It is shown that the off-diagonal chemical exchange peaks have shapes that are a combination (outer product) of the absorption line shapes of the species that give rise to the diagonal peaks.     

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.     

Infrared spectra of a model phenol-amine proton transfer complex in nanoconfined CH3Cl

The vibrational spectra of a model phenol-amine proton transfer complex dissolved in CH3Cl solvent confined in a 12 A radius spherical hydrophobic cavity were calculated using mixed quantum-classical molecular dynamics simulations. The reaction free energy of the proton transfer complex was varied in order to explore the contributions to the vibrational absorption band from product and reactant species. The vibrational spectra of the model proton transfer complex resulted in motionally narrowed spectral linewidths with two distinct peaks for products and reactants in cases where the system undergoes chemical exchange. It was found that the n=1 and n=2 vibrational excited states combine to form diabatic states such that the spectra have contributions from both n=0 --> n=1 and n=0 --> n=2 transitions. A strong relationship between the instantaneous vibrational frequency and a collective solvent coordinate was found that assists in understanding the origin of the spectral features.     

Solute-solvent complex switching dynamics of chloroform between acetone and dimethylsulfoxide-two-dimensional IR chemical exchange spectroscopy

Hydrogen bonds formed between C-H and various hydrogen bond acceptors play important roles in the structure of proteins and organic crystals, and the mechanisms of C-H bond cleavage reactions. Chloroform, a C-H hydrogen bond donor, can form weak hydrogen-bonded complexes with acetone and with dimethylsulfoxide (DMSO). When chloroform is dissolved in a mixed solvent consisting of acetone and DMSO, both types of hydrogen-bonded complexes exist. The two complexes, chloroform-acetone and chloroform-DMSO, are in equilibrium, and they rapidly interconvert by chloroform exchanging hydrogen bond acceptors. This fast hydrogen bond acceptor substitution reaction is probed using ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy. Deuterated chloroform is used in the experiments, and the 2D-IR spectrum of the C-D stretching mode is measured. The chemical exchange of the chloroform hydrogen bonding partners is tracked by observing the time-dependent growth of off-diagonal peaks in the 2D-IR spectra. The measured substitution rate is 1/30 ps for an acetone molecule to replace a DMSO molecule in a chloroform-DMSO complex and 1/45 ps for a DMSO molecule to replace an acetone molecule in a chloroform-acetone complex. Free chloroform exists in the mixed solvent, and it acts as a reactive intermediate in the substitution reaction, analogous to a SN1 type reaction. From the measured rates and the equilibrium concentrations of acetone and DMSO, the dissociation rates for the chloroform-DMSO and chloroform-acetone complexes are found to be 1/24 ps and 1/5.5 ps, respectively. The difference between the measured rate for the complete substitution reaction and the rate for complex dissociation corresponds to the diffusion limited rate. The estimated diffusion limited rate agrees well with the result from a Smoluchowski treatment of diffusive reactions.     

Gas phase solvatochromic effects of phenol and naphthol photoacids

A quantum chemical study of spectral shifts by single molecule solvation of phenol, α-naphthol, and β-naphthol is presented. The methods employed include the equation-of-motion coupled cluster, the similarity transformed equation-of-motion coupled cluster, single excitation configuration-interaction, and time-dependent density functional theory. Based on the calculations, there is no evidence that there is significant charge-transfer between the solute and the solvent. Instead, it appears that the observed solvation redshift is due to the nature of the excited state on the solute molecule.     

Excitation transfer induced spectral diffusion and the influence of structural spectral diffusion

The theory of vibrational excitation transfer, which causes spectral diffusion and is also influenced by structural spectral diffusion, is developed and applied to systems consisting of vibrational chromophores. Excitation transfer induced spectral diffusion is the time-dependent change in vibrational frequency induced by an excitation on an initially excited molecule jumping to other molecules that have different vibrational frequencies within the inhomogeneously broadened vibrational absorption line. The excitation transfer process is modeled as Fo?rster resonant transfer, which depends on the overlap of the homogeneous spectra of the donating and accepting vibrational chromophores. Because the absorption line is inhomogeneously broadened, two molecules in close proximity can have overlaps of their homogeneous lines that range from substantial to very little. In the absence of structural dynamics, the overlap of the homogeneous lines of the donating and accepting vibrational chromophores would be fixed. However, dynamics of the medium that contains the vibrational chromophores, e.g., a liquid solvent or a surrounding protein, produce spectral diffusion. Spectral diffusion causes the position of a molecule's homogeneous line within the inhomogeneous spectrum to change with time. Therefore, the overlap of donating and accepting molecules' homogeneous lines is time dependent, which must be taken into account in the excitation transfer theory. The excitation transfer problem is solved for inhomogeneous lines with fluctuating homogeneous line frequencies. The method allows the simultaneous treatment of both excitation transfer induced spectral diffusion and structural fluctuation induced spectral diffusion. It is found that the excitation transfer process is enhanced by the stochastic fluctuations in frequencies. It is shown how a measurement of spectral diffusion can be separated into the two types of spectral diffusion, which permits the structural spectral diffusion to be determined in the presence of excitation transfer spectral diffusion. Various approximations and computational methodologies are explored.     

H2O and D2 mixtures under pressure: spectroscopy and proton exchange kinetics

We have investigated the pressure-induced spectral changes and the proton exchange reactions of D(2)-H(2)O mixtures to 64 GPa using micro-Raman spectroscopy. The results show the profound difference in the rotational and vibrational Raman spectra of hydrogen isotopes from those of the pure samples, showing the vibrational modes at higher frequencies and continuing to increase with pressure without apparent turnover. This indicates the repulsive nature of D(2)-H(2)O interaction without hydrogen bonds between the two and, thus, interstitial fillings of D(2) molecules into the bcc-like ice lattice. The spectral analysis using the Morse potential yields a hydrogen bond distance of 0.734 ? at 6 GPa--slightly shorter than that in pure--attributed to the repulsive interaction. The pressure-dependent spectral changes suggest that the proton-ordering transition in the ice lattice occurs over a large pressure range between 28 and 50 GPa, which is substantially lower than that of pure ice (40-80 GPa). This again indicates the presence of high internal pressure arising from the repulsive interaction. The Raman spectra show evidences that the proton exchange occurs in various phases including in solid D(2) and H(2)O mixtures. Based on the time-dependent spectral changes, we obtained the proton exchange rates of k ~ 0.085 h(-1) at 0.2 GPa in fluid D(2) and water mixtures, k ~ 0.03 h(-1) and 0.003 h(-1) at 2 GPa and 4 GPa, respectively, in fluid D(2)-ice mixtures, and k ~ 10(-3) h(-1) at 8 GPa in solid D(2) and ice mixtures.     

Ultrafast vibrational dynamics of adenine-thymine base pairs in DNA oligomers

N-H stretching excitations of DNA oligomers containing 23 alternating adenine-thymine base pairs are studied in femtosecond two-color pump-probe experiments. For a DNA film in a zero relative humidity atmosphere, transient vibrational spectra and their time evolution up to 10 ps demonstrate negligible spectral diffusion and allow for discerning different N-H stretching bands and the O-H stretching absorption of residual water molecules. Lifetimes on the order of 0.5 ps are found for both N-H and O-H stretching modes. The time-dependent pump-probe anisotropies of the different N-H excitations point to a pronounced coupling among them, whereas the O-H stretching anisotropy remains essentially constant.     

Cross‐Peaks in Simple Two‐Dimensional NMR Experiments from Chemical Exchange of Transverse Magnetisation

Two‐dimensional correlation measurements such as COSY, NOESY, HMQC, and HSQC experiments are central to small‐molecule and biomolecular NMR spectroscopy, and commonly form the basis of more complex experiments designed to study chemical exchange occurring during additional mixing periods. However, exchange occurring during chemical shift evolution periods can also influence the appearance of such spectra. While this is often exploited through one‐dimensional lineshape analysis (“dynamic NMR”), the analysis of exchange across multiple chemical shift evolution periods has received less attention. Here we report that chemical exchange‐induced cross‐peaks can arise in even the simplest two‐dimensional NMR experiments. These cross‐peaks can have highly distorted phases that contain rich information about the underlying exchange process. The quantitative analysis of such peaks, from a single 2D spectrum, can provide a highly accurate characterisation of underlying exchange processes.     

Density functional theory (DFT) calculations of the infrared absorption spectra of acetaminophen complexes formed with ethanol and acetone species

We have investigated the infrared (IR) vibrational spectra of acetaminophen (N(4-hydroxyphenyl) acetamide or paracetamol) complexes formed with ethanol and acetone in relation to the nature of the specific intermolecular interactions involved in the stabilization of the complexes. The structures and binding energies of the complexes have been determined using Hartree-Fock (HF) and DFT-B3PW91 procedures and different Pople's basis sets as well. The main results are presented and discussed by considering the hydroxyl (OH), amino (NH), and carbonyl (CO) chemical groups of acetaminophen interacting with the acetone or ethanol molecules either separately or in conjunction in the complex formation. The frequency shifts and IR intensity variations associated with the internal modes of acetaminophen (namely nu(OH), nu(NH), and nu(CO)) as well as the most pertinent vibrational probes of ethanol (nu(OH)) and acetone (symmetric nu(CO) and nu(CCC) stretching modes) interacting with acetaminophen have been analyzed. The predicted spectral changes have been critically discussed in comparison with IR absorption measurements of acetaminophen dissolved as a solute in ethanol or acetone CO2 expanded solutions. It is argued that the exchange-correlation contribution taken into account in DFT calculations is likely significant in determining the main IR spectral features of acetaminophen complexes formed with acetone or involving hydrogen-bonded as with ethanol.     

Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes

In this and the following paper, we describe the ultrafast structural fluctuations and rearrangements of the hydrogen bonding network of water using two-dimensional (2D) infrared spectroscopy. 2D IR spectra covering all the relevant time scales of molecular dynamics of the hydrogen bonding network of water were studied for the OH stretching absorption of HOD in D2O. Time-dependent evolution of the 2D IR line shape serves as a spectroscopic observable that tracks how different hydrogen bonding environments interconvert while changes in spectral intensity result from vibrational relaxation and molecular reorientation of the OH dipole. For waiting times up to the vibrational lifetime of 700 fs, changes in the 2D line shape reflect the spectral evolution of OH oscillators induced by hydrogen bond dynamics. These dynamics, characterized through a set of 2D line shape analysis metrics, show a rapid 60 fs decay, an underdamped oscillation on a 130 fs time scale induced by hydrogen bond stretching, and a long time decay constant of 1.4 ps. 2D surfaces for waiting times larger than 700 fs are dominated by the effects of vibrational relaxation and the thermalization of this excess energy by the solvent bath. Our modeling based on fluctuations with Gaussian statistics is able to reproduce the changes in dispersed pump-probe and 2D IR spectra induced by these relaxation processes, but misses the asymmetry resulting from frequency-dependent spectral diffusion. The dynamical origin of this asymmetry is discussed in the companion paper.     

Formation and dissociation of intra-intermolecular hydrogen-bonded solute-solvent complexes: chemical exchange two-dimensional infrared vibrational echo spectroscopy

2-Methoxyphenol (2MP) solutes form weak complexes with toluene solvent molecules. The complexes are unusual in that the 2MP hydroxyl has an intramolecular hydrogen bond and simultaneously forms an intermolecular hydrogen bond with toluene and other aromatic solvents. In the equilibrated solute-solvent solution, there exists approximately the same concentration of 2MP-toluene complex and free 2MP. The very fast formation and dissociation (chemical exchange) of this type of three-centered hydrogen bond complex were observed in real time under thermal equilibrium conditions with two-dimensional (2D) infrared vibrational echo spectroscopy. Chemical exchange is manifested in the 2D spectrum by the growth of off-diagonal peaks. Both the formation and dissociation can be characterized in terms of the dissociation time constant, which was determined to be 3 ps for the 2MP-toluene complex. The intra-intermolecular hydrogen bond formation is influenced by subtle details of the molecular structure. Although 2MP forms a complex with toluene, it is demonstrated that 2-ethoxyphenol (2EP) does not form complexes to any significant extent. Density functional calculations at the B3LYP/6-31+G(d,p) level suggest that steric effects caused by the extra methyl group in 2EP are responsible for the difference.     

COORDINATION COMPOUNDS OF LANTHANIDE PERCHLORATES WITH PYRAZINEAMIDE

Abstract

Lanthanide perchlorate complexes of the type [Ln(pyaH)₄] (ClO₄)₃ where Ln=Pr, Nd, Sm, Eu, Tb and Lu, and pyaH is pyrazinamide have been isolated. The compounds were characterized by chemical analyses, molar conductance, vibrational spectra, and electronic absorption and emission spectra. The vibrational spectra and molar conductances indicate that the perchlorate groups are ionic and that pyaH acts a bidentate ligand. The oscillator strengths of the transitions of the Nd(III) complex were determined in terms of the Judd-Ofelt theory. It was possible to use the modified Judd-Ofelt parameters, τλ, for the evaluation of the spectral intensities. In addition, a group-theoretical analysis of the emission spectrum indicates an effective site symmetry D₂ for the Eu(III) complex between 77° K and 10° K.     

Hydrophobic molecules slow down the hydrogen-bond dynamics of water

We study the spectral and orientational dynamics of HDO molecules in solutions of tertiary-butyl-alcohol (TBA), trimethyl-amine-oxide (TMAO), and tetramethylurea (TMU) in isotopically diluted water (HDO:D(2)O and HDO:H(2)O). The spectral dynamics are studied with femtosecond two-dimensional infrared spectroscopy and the orientational dynamics with femtosecond polarization-resolved vibrational pump-probe spectroscopy. We observe a strong slowing down of the spectral diffusion around the central part of the absorption line that increases with increasing solute concentration. At low concentrations, the fraction of water showing slow spectral dynamics is observed to scale with the number of methyl groups, indicating that this effect is due to slow hydrogen-bond dynamics in the hydration shell of the methyl groups of the solute molecules. The slowing down of the vibrational frequency dynamics is strongly correlated with the slowing down of the orientational mobility of the water molecules. This correlation indicates that these effects have a common origin in the effect of hydrophobic molecular groups on the hydrogen-bond dynamics of water.     

Vibrational analysis of free and hydrogen bonded complexes of nicotinamide and picolinamide

Harmonic and anharmonic vibrations of free nicotinamide (NIA) and picolinamide (PIA) molecules together with their hydrogen bonded complexes H₂O–NIA and H₂O–PIA have been studied by means of density functional method. The calculation results of the vibrational spectra of free molecules have been investigated and are compared to the available experimental spectra. The vibrational wavenumbers of both molecules have also been calculated by polarizable continuum model (PCM) that represents the solvent as a polarizable continuum and places the solute in a cavity within the solvent (water is chosen as the solvent in this study). The results of PCM calculations and the H₂O–NIA, H₂O–PIA complexes, are used to investigate the H-bonding interactions of both molecules with the water molecule. The harmonic wavenumbers have been scaled by proper factors obtained by comparing the observed versus calculated wavenumbers and it is shown that anharmonic corrections on the vibrational spectra provided a better agreement between the observed and calculated wavenumbers compared to the results obtained by scaling factor method.     

Resonance Raman and surface-enhanced resonance Raman spectra of LH2 antenna complex from Rhodobacter sphaeroides and Ectothiorhodospira sp. excited in the Qx and Qy transitions

Well-resolved vibrational spectra of LH2 complex isolated from two photosynthetic bacteria, Rhodobacter sphaeroides and Ectothiorhodospira sp., were obtained using surface-enhanced resonance Raman scattering (SERRS) exciting into the Qx and the Qy transitions of bacteriochlorophyll a. High-quality SERRS spectra in the Qy region were accessible because the strong fluorescence background was quenched near the roughened Ag surface. A comparison of the spectra obtained with 590 nm and 752 nm excitation in the mid- and low-frequency regions revealed spectral differences between the two LH2 complexes as well as between the LH2 complexes and isolated bacteriochlorophyll a. Because peripheral modes of pigments contribute mainly to the low-frequency spectral region, frequencies and intensities of many vibrational bands in this region are affected by interactions with the protein. The results demonstrate that the microenvironment surrounding the pigments within the two LH2 complexes is somewhat different, despite the fact that the complexes exhibit similar electronic absorption spectra. These differences are most probably due to specific pigment-pigment and pigment-protein interactions within the LH2 complexes, and the approach might be useful for addressing subtle static and dynamic structural variances between pigment-protein complexes from different sources or in complexes altered chemically or genetically.     

Antioxidant and Biochemical Activities of Mixed Ligand Complexes

Novel 4-aminoantipyrine based mixed ligand metal complexes with the Schiff bases ofL¹(L¹-4(furanylmethyleneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one and L²/ L³/ L⁴are 2-(2-chlorobenzylideneamino)phenol, 2-(3-chlorobenzylideneamino)phenol, 2-(4-chlorobenzylideneamino)phenol were synthesized. The structures of the mixed ligand complexes were established by analytical and spectral techniques. They were screened for in vitro antimicrobial activity against bacteria and fungi by disc diffusion method. The interaction of metal complexes with CT-DNA was investigated by UV–vis, cyclic voltammetry, viscosity and thermal denaturation studies.DNA interaction studies suggest that metal complex binds to calf thymus DNA (CT-DNA) through intercalation mode. Superoxide dismutase activity of these complexes has also been studied. The free ligands and their metal complexes have been tested for in vitro antioxidant activity by the reduction of 1,1-diphenyl-2-picryl hydrazyl (DPPH).The antioxidant activities of the complexes were studied and compared with the activity of ascorbic acid. Cu(II) complex showed superior antioxidant activity than other complexes. The solvatochromic behaviour of complexes was also performed in various solvents.     

Ultrasonic and IR study of molecular association process through hydrogen bonding in ternary liquid mixtures

Complex formation in ternary liquid mixtures of heterocyclic compounds, viz. pyridine and quinoline with phenol in benzene has been studied through ultrasonic velocity measurements (at 2 MHz) in the concentration range of 0.010–0.090 at varying temperatures of 35, 45 and 55 °C. The ultrasonic velocity and density data are used to estimate adiabatic compressibility, intermolecular free length, molar sound velocity, molar compressibility and specific acoustic impedance. These acoustical parameters, in turn, are used to study the solute–solute interactions in these systems. The ultrasonic velocity shows a maxima and adiabatic compressibility a corresponding minima as a function of concentration for these mixtures. The results indicate the possible occurrence of complex formation between unlike molecules through intermolecular hydrogen bonding between the nitrogen atom of pyridine and quinoline molecules and the hydrogen atom of phenol molecule. Further, the excess values of adiabatic compressibility and intermolecular free length have also been evaluated and discussed in relation to complex formation. The infrared spectra of both the systems, pyridine–phenol and quinoline–phenol, have been also recorded for various concentrations at room temperature (35 °C) and found to be useful for understanding the presence of N⋯HO bond complexes and the strength of molecular association at specific concentrations.     

Vibrational spectra of palladium 5-nitrofuryl thiosemicarbazone complexes: experimental and theoretical study

The vibrational spectroscopic behavior of a series of 16 palladium(II) complexes with 8 bioactive nitrofuran containing thiosemicarbazones as ligands has been studied in the solid state. The IR and Raman spectra of these complexes and the free nitrofuran thiosemicarbazone ligands were recorded and analyzed. Experimental spectra were satisfactorily described by density functional theory (DFT) calculations. The combination of experimental and theoretical methods allowed us to perform the characterization of the main vibrations that show the mode of coordination of the thiosemicarbazone moiety to palladium even though these vibration bands are located in spectral regions showing a complicated pattern due to the presence of vibrations of the nitrofuran moiety and combination modes involving furan vibrations. A characteristic vibrational spectroscopic pattern has been defined for Pd(II) 5-nitrofuryl thiosemicarbazone complexes. This systematic knowledge may be useful for the analysis of the spectroscopic behavior of other coordination compounds holding the 5-nitrofuran thiosemicarbazone moiety.