H-bonded NH Research Articles

Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 310-helix former.

The conformational preferences of a series of capped peptides containing the helicogenic amino acid aminoisobutyric acid (Aib) (Z-Aib-OH, Z-(Aib)2-OMe, and Z-(Aib)4-OMe) are studied in the gas phase under expansion-cooled conditions. Aib oligomers are known to form 310-helical secondary structures in solution and in the solid phase. However, in the gas phase, accumulation of a macrodipole as the helix grows could inhibit helix stabilization. Implementing single-conformation IR spectroscopy in the NH stretch region, Z-Aib-OH and Z-(Aib)2-OMe are both observed to have minor conformations that exhibit dihedral angles consistent with the 310-helical portion of the Ramachandran map (ϕ, ψ = -57°, -30°), even though they lack sufficient backbone length to form 10-membered rings which are a hallmark of the developed 310-helix. For Z-(Aib)4-OMe three conformers are observed in the gas phase. Single-conformation infrared spectroscopy in both the NH stretch (Amide A) and C[double bond, length as m-dash]O stretch (Amide I) regions identifies the main conformer as an incipient 310-helix, having two free NH groups and two C10 H-bonded NH groups, labeled an F-F-10-10 structure, with a calculated dipole moment of 13.7 D. A second minor conformer has an infrared spectrum characteristic of an F-F-10-7 structure in which the third and fourth Aib residues have ϕ, ψ = 75°, -74° and -52°, 143°, Ramachandran angles which fall outside of the typical range for 310-helices, and a dipole moment that shrinks to 5.4 D. These results show Aib to be a 310-helix former in the gas phase at the earliest stages of oligomer growth.

Building Up Water-Wire Clusters: Isomer-Selective Ultraviolet and Infrared Spectra of Jet-Cooled 2-Aminopurine (H2O)n, n = 2 and 3

2-Aminopurine (2AP) is an adenine analogue with a high fluorescence quantum yield in water solution, which renders it a useful real-time probe of DNA structure. We report the ultraviolet (UV) and infrared (IR) spectra of size-selected and jet-cooled 9H-2AP·(H2O)n clusters with n = 2 and 3. Mass- and species-specific UV/UV holeburning spectroscopy allows to separate the UV spectra of four cluster isomers in the 31,200–33,000 cm(–1) spectral region with electronic band origins at 31339, 31450, 31891, and 32163 cm(–1). Using IR/UV depletion spectroscopy in combination with B3LYP calculated harmonic vibrational frequencies, the H-bonding topologies of two isomers of the n = 2 and of two isomers of the n = 3 cluster are identified. One n = 2 isomer (denoted 2A) forms a water dimer chain between the N9H and N3 atoms at the sugar-edge site, the other isomer (denoted 2D) binds one H2O at the sugar-edge site and the other at the trans-amino site between the N1 atom and the NH2 group. For 2-aminopurine·(H2O)3, one isomer (denoted 3A) forms an H-bonded water wire at the sugar-edge site, while isomer 3B accommodates two H2O molecules at the sugar-edge and one at the trans-amino site. The approximate second-order coupled cluster (CC2) method predicts the adiabatic S1 ← S0 transitions of 9H-2-aminopurine and six water cluster isomers with n = 1–3 in very good agreement with the experimental 0(0)(0) frequencies, with differences of <0.6%. The stabilization of the S1(ππ*) state of 2-aminopurine by water clusters is highly regiospecific: Isomers with one or two H2O molecules H-bonded in the trans-amino position induce large spectra red shifts, corresponding to 1ππ* state stabilization of 10–12 kJ/mol, while water-wire cluster solvation at the sugar-edge leads to much smaller stabilization. The evolution of the IR spectra of the water-wire clusters with n = 1–3 that are H-bonded to the sugar-edge site is discussed. Qualitatively different regions (denoted I to IV) can be attributed to the different free and H-bonded OH, NH, NH2 and OH···OH water-wire stretch vibrations.

Identification of dissolved organic matter in raw water supply from reservoirs and canals as precursors to trihalomethanes formation

The characteristic and quantity of dissolved organic matter (DOM) as trihalomethanes precursors in water from the U-Tapao Basin, Songkhla, Thailand was investigated. The sources of water in the basin consisted of two reservoirs and the U-Tapao canal. The canal receives water discharge from reservoirs, treated and untreated wastewater from agricultural processes, communities and industries. Water downstream of the canal is utilized as a raw water supply. Water samples were collected from two reservoirs, upstream and midstream of the canal, and the raw water supply in the rainy season and summer. The DOM level in the canal water was higher than that of the reservoir water. The highest trihalomethane formation potential (THMFP) was formed in the raw water supply. Fourier-transform infrared peaks of the humic acid were detected in the reservoir and canal waters. Aliphatic hydrocarbon and organic nitrogen were the major chemical classes in the reservoir and canal water characterized by a pyrolysis gas chromatography mass spectrometer. The optimal condition of the poly aluminum chloride (PACl) coagulation was obtained at a dosage of 40 mg/L at pH 7. This condition could reduce the average UV-254 to 57%, DOC to 64%, and THMFP to 42%. In the coagulated water, peaks of O-H groups or H-bonded NH, C˭O of cyclic and acyclic compounds, ketones and quinines, aromatic C˭C, C-O of alcohols, ethers, and carbohydrates, deformation of COOH, and carboxylic acid salts were detected. The aliphatic hydrocarbon, organic nitrogen and aldehydes and ketones were the major chemical classes. These DOM could be considered as the prominent DOM for the water supply plant that utilized PACl as a coagulant.

Investigation of folding patterns in homo-oligomers of (R)-β2,2-amino acids with carbohydrate side chain

The study describes the synthesis of new β2,2-peptides made from geminally disubstituted β2,2-amino acid and their folding propensities. The (R)-C-linked carbo-β2,2-amino acid [(R)-β2,2-Caa] was prepared from d-glucose and converted into the homo-oligomeric di-, tetra-, and hexapeptides. The conformational studies were carried out using NMR (in CDCl3), CD, IR, and MD calculations. These β2,2-peptides were interestingly stabilized by five-membered (mr) inter-residue H-bonds NH(i)⋯O(i-1) (furanoside) and a 6-mr intra-residue H-bond between amide proton (NH(i)) and the oxygen of –OMe(i) at the C3 carbon of the carbohydrate side chain. These results amply demonstrate that the ‘epimerization’ at the spiro carbon center has an effect on the conformational behavior of these peptides. Finding of these, H-bonding patterns, which are not so common to stabilize the folds in this class of β2,2-Caa derived peptides would further facilitate augmentation in the domain of foldamer.

Contribution of the π electron to the N–H⋯OC hydrogen bond: IR spectroscopic studies of the jet-cooled pyrrole–acetone binary clusters

To investigate the π bonding electron contribution to N-H···O=C hydrogen-bond (H-bond) formation, we applied IR cavity ringdown spectroscopy to jet-cooled pyrrole-acetone (Py-Ac) binary clusters. The observed NH stretching vibrations were analyzed by density functional theory (DFT), in which the energetically optimized structures, harmonic frequencies, and interaction energies were calculated for various sizes of binary clusters. We observed three NH stretching vibrations, ascribed to binary clusters at 3406, 3388, and 3335 cm(-1). These were assigned to H-bonded NH stretches of the Py(2)-Ac(1), Py(1)-Ac(1), and Py(1)-Ac(2) clusters, respectively. The Py(1)-Ac(1) cluster has a single N-H···O=C H-bonded structure with C(s) symmetry, while the Py(1)-Ac(2) cluster has a cyclic structure formed by a single N-H···O=C H-bond, dipole-dipole interactions, and weak CH H-bonds. A natural bond orbital (NBO) analysis was performed to reveal the H-bond strength in Py-Ac binary clusters. For the Py(1)-Ac(2) cluster, we found that the donor-acceptor interactions are not only the n →σ* type (O atom lone pair to the NH anti-bonding orbitals), but also the π→σ* type (the CO π bonding to the NH anti-bonding orbitals). By analyzing the relationship between the frequency shift and the stabilization energy in donor-acceptor interactions, we concluded that larger red-shift of the NH stretching vibration in the Py(1)-Ac(2) can be explained by not only the lone pair and the π electron contributions to the N-H···O=C H-bond, but also the dipole-interaction between Py and non-H-bonded Ac. We also discussed the structures of Py(2)-Ac(1) clusters.

Hydrogen-bonded structures for self-aggregates of 2,5-dimethylpyrrole and its binary clusters with pyrrole studied by IR cavity ringdown spectroscopy

N-H···π hydrogen-bonded (H-bonded) structures were studied by applying vibrational spectroscopy to self-aggregate clusters of 2,5-dimethylpyrrole (DMPy) and its binary clusters with pyrrole (Py). The NH stretching vibrations of jet-cooled clusters were observed by IR cavity ringdown spectroscopy. A combination of experiments and density functional theory calculations revealed the stable structures, intermolecular binding energies, and harmonic vibrational frequencies. The IR spectrum of the DMPy self-aggregate clusters was very similar in spectral features to that of the Py clusters in a previous work. The observed NH stretching vibrations at 3505, 3420, 3371, and 3353 cm(-1) are simultaneously red-shifted by ∼25 cm(-1) from the Py monomer, dimer, trimer, and tetramer, respectively. Based on a spectral analogy of DMPy with Py, and a consistency of the calculated harmonic frequencies with experiments, the H-bonded structures of the DMPy clusters were determined to be of a T-shape for a dimer and a cyclic for a trimer and a tetramer. For the DMPy-Py binary clusters, we discussed the stability and geometry of the N-H···π interactions in the T-shaped dimer and the cyclic trimer. The binary dimer showed the only single NH stretch at 3419 cm(-1) in the IR spectrum. A vibrational analysis of the H-bonded NH stretches as well as the calculated stabilization energies deduced that only the binary dimer by DMPy as an acceptor and Py as a donor can exist in a supersonic jet. For binary trimers, NH stretches were observed due to both (DMPy)(2)-(Py)(1) and (DMPy)(1)-(Py)(2). They were found to have different vibrational patterns from each other; the former showed three dispersed NH stretches, and the other had two quasi-degenerate NH stretches. Throughout this study, we also considered the intermolecular geometries, such as the H-bond distance and the angle in terms of the methyl group substitution effect.

Ammonia‐Solvated Ammonium Species in the NH4‐ZSM‐5 Zeolite

Interaction of gaseous ammonia with a NH(4)-ZSM-5 zeolite (Si/Al=11.5) was studied by means of infrared (IR) spectroscopy both at constant ambient temperature and in the temperature range 373-573 K. H-bonding of NH(3) molecules to the NH(4) (+) species takes place. The interaction is weak and reversible, resembling a solvation process. Spectral evidence shows that only one N--H moiety is actually available, indicating that ammonium ions are tricoordinated to the zeolite inner surface. H-bonded NH(3) has an absorption band at 1712 cm(-1), which grows with increasing pressure in two steps: a monosolvated ammonium species is initially formed, evolving to a disolvated species for pressures above 5 mbar. Coordination of the second NH(3) molecule takes place at the already coordinated NH(3) molecule and not at the ammonium cation. From the changes in intensity of the 1712 cm(-1) band with changing temperature under a moderate NH(3) equilibrium pressure, the calculated standard enthalpy and entropy of the monosolvation reaction were ΔH(0)=-34(±5) kJ mol(-1) and ΔS(0)=-88(±10) J mol(-1) K(-1), respectively. The enthalpy of the second solvation step was calculated from the corresponding equilibrium constant under the assumption of (nearly) the same entropy change for both solvation processes. In agreement with the overall picture, this enthalpy change is small (-15 kJ mol(-1) at the most). Since in a previous work (M. Armandi, B. Bonelli, I. Bottero, C. O. Areán, E. Garrone, J. Phys. Chem. C 2010, 114, 6658) the thermodynamic features of the reaction between bare Brønsted acid sites and NH(3) yielding NH(4) (+) species were determined, the data reported herein allow the study of the coexistence of different species in the NH(3)/H-ZSM-5 zeolite system: 1) unreacted acid Brønsted sites, 2) bare ammonium ions, and 3) variously solvated ammonium species. The relevant description is particularly simple when the overall average coverage is one molecule per site.

Synthesis and crystal structure of N,N-dimethylbiguanidinium hexafluorosilicate

The complex [(CH3)2NC(NH2)NHC(NH2)NH2]SiF6 (I) was synthesized and its structure was determined by X-ray crystallography. The crystals are monoclinic: a = 7.4346(10) A, b = 12.7628(10) A, c = 11.0828(10) A, β 104.080(10)°, V = 1020.01(18) A3, ρcalc = 1.780 g/cm3, μ(MoKα) = 0.302 mm−1, Z = 4, space group P21/c. The crystals of I are composed of SiF62− anions (Si-F, 1.657(2)–1.699(2) A) and N,N-dimethylbiguanidinium (H2L2+) cations combined in a framework by interionic H-bonds NH···F. In the cations, protonation sites are the terminal imide groups.

Effect of a pH Change on the Conformational Stability of the Modified Nucleotide Queuosine Monophosphate

The naturally occurring modified nucleotide queuosine 5'-monophosphate (QMP) related to biochemical regulatory pathways in the cell was investigated using quantum chemical approaches. The relative stability of biologically relevant conformations of QMP in solvent under a pH change was predicted at the BVP86/TZVP and MP2/TZVP levels of theory. Hydrogen bonding in QMP was studied using Bader's approach. The acidity constants of QMP were estimated using the COSMO-RS theory. It has been found that the neutral and anionic forms of QMP are the most stable in the physiological pH range. These forms correspond to the anti/north conformation and exist as zwitterionic tautomers having a negatively charged phosphate group (-1 for neutral and -2 for anionic) and a positively charged secondary amine group in the side chain. It was also found that QMP possesses the syn conformation in the cationic state at pH < 5.0 and undergoes syn to anti conformation transition when the pH increases, remaining in the anti conformation at the higher pH values. The marker IR bands specific for the anionic and neutral QMP forms in the 2300-2700 cm(-1) region were assigned to H-bonded NH groups of the QMP side chain. The bands between 800 and 1300 cm(-1) of the "fingerprint" (400-1500 cm(-1)) region were assigned to the vibrations of the ribose ring, the phosphate group and the side chain of QMP. The predicted IR spectra can be useful for the assignment of vibration bands in the experiential spectra of QMP or identification of the QMP forms. The revealed peculiarities of the QMP conformation sensitivity to a pH change as well as additional formed H-bonds could be responsible for specific nucleotide interactions with enzymes.

Detection of trivalent arsenic [As(III)] complex with DNA: A spectroscopic investigation

Arsenite [As(III)] is well known to exert mutagenic or carcinogenic effects. Arsenic (III) binds proteins with its cystine–SH group to DNA. Overall binding constant K = 1.12 × 104 M−1 and exponential decay constant T 1 = 271 s for DNA–As (III) interaction were measured spectrophometrically at λ max = 260 nm. Fourier transform infrared (FTIR) spectrometric method was used to charac-terize and determine the arsenite binding site in DNA–As(III) interaction. FTIR spectroscopic results showed that As(III) indirectly binds to the nitrogen bases of DNA and predominantly affected the H-bonded OH and NH bands, whereas no interaction was found with phosphate groups. No transitions from B to A or B to Z was observed in B-DNA structure.

Hydrogen-bonding interaction in a complex of amino acid with urea studied by DFT calculations

Theoretical studies on hydrogen-bonded complexes between amino acids (glycine, alanine, and leucine) and urea in gas phase have been carried out using density functional theory (DFT) and ab initio methods at the B3LYP/6-311++g** and MP2/6-311++g** theory levels. The structures, binding energy, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution, and bond characteristics of the mentioned complexes were calculated. Urea is a good H-bond donor and an excellent receptor for highly electronegative atoms like O and N, through the formation of two or more hydrogen bonds. The NH2 and COOH groups of amino acids can form several different types of H-bonds with urea molecular, as well as CαH and alkyl side chains. The calculated high binding energy also suggests multiple H-bonds formed in one complex. The OH···O contact is the strongest hydrogen bond interaction with H···O separation around 1.65 A and its relevant angle close to 176°. The closely linear amide H-bonds NH···O and OH···N strongly stabilize the amino acid–urea complex with H···O separation between 1.89 and 2.38 A. The weaker CH···O/N H-bonds are also discussed as significant interaction in biological systems involving amino acids.

Theoretical Study on Dihydrogen Bonds of NH3BH3 with Several Small Molecules

The dihydrogen bonds BH H-X (X = F, Cl, Br, C, O, N) in the dimer (NH3BH3)2 and the complexes of NH3BH3 with HF, HCl, HBr, H2CO, H2O, and CH3OH were theoretically studied. The results show that formation of the dihydrogen bond leads to elongation and stretch frequency red shift of the BH and XH bonds, except that in the H2CO system, the CH bond blue shifts. For (NH3BH3)2 and the complexes of the halogenides, red shifts of the XH bonds are caused by the intermolecular hyperconjugation (BH) * (XH). For the system of H2CO, a blue shift of the CH bond is caused by a decrease of the intramolecular hyperconjugation n(O) *(CH). In the other two systems, the red shift of OH bond is a secondary effect of the stronger traditional red-shifted H-bonds NH O. In all these systems, red shifts of the BH bonds are caused by two factors: negative repolarization and negative rehybridization of the BH bond, and decrease of occupancy on (BH) caused by the intermolecular hyperconjugation (BH)*(XH).

Crystal structure of bis(3-carboxypyridinium) hexafluorosilicate

Complex [3-HO(O)CC5H4NH]2SiF6 is synthesized, and its structure is determined by single-crystal X-ray diffraction. In its ionic structure, the centrosymmetric SiF62− anions (the Si-F bond lengths are 1.6658(15)–1.7033(17) A) and [3-HO(O)CC5H4NH]+ cations are linked through interionic H-bonds NH…F, NH…O, and OH…F (the N…F, N…O, and O…F distances are 2.752(3), 2.935(3), and 2.596(2) A, respectively).

Ab Initio Study of the Microscopic Mechanism Leading to Antiferroelectricity in NH4H2PO4 (ADP)

The microscopic mechanim leading to a low-temperature antiferroelectric (AFE) phase in H-bonded NH 4 H2PO 4 is studied by means of first-principles calculations in the framework of the Density Functional Theory. We compute the total energy for atomic displacements following the ferroelectric (FE) and AFE mode patterns and also constraining the atoms in different cases. We calculate Mulliken populations for atoms and orbitals to show the important charge transfers and instabilities of the system. The AFE phase appears as a consequence of the H ordering in the O─H─O bridges leading to polarizations of the H 2 PO 4 perpendicular to the tetragonal crystal axis and alternating in chains. It is found that the formation of N─H─O bridges with correlated charge transfers is essential in stabilizing this configuration against a FE phase polarized along the tetragonal axis, as e.g. in KH 2 PO 4 (KDP). We also study de closeness of FE with AFE configuration energies and other hypothetical phases, which may explain the experimental detection of signals arising from small FE defects in the PE phase near the transition.

Single-Conformation Ultraviolet and Infrared Spectroscopy of Model Synthetic Foldamers: β-Peptides Ac-β3-hPhe-NHMe and Ac-β3-hTyr-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-NHMe (1) and Ac-beta3-hTyr-NHMe (2), have been explored under jet-cooled, isolated molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl or phenol ring substituents, respectively. UV-UV hole-burning spectroscopy was used to determine that two conformations of 1 are present, with the transitions due to conformer A, with S0-S1 origin at 34431 cm(-1), being almost 20 times larger than those due to conformer B, with S0-S1 origin at 34404 cm(-1). Only one conformation of 2 was observed. Resonant ion-dip infrared spectroscopy provided single-conformation infrared spectra in the 3300-3700 cm(-1) region. The spectra of conformer A of both molecules have H-bonded and free amide NH stretch infrared transitions at 3400 and 3488 cm(-1), respectively, while conformer B of 1 possesses bands at 3417 and 3454 cm(-1). For comparison with experiment, full optimizations of all low-lying minima of 1 were carried out at the DFT B3LYP/6-31+G* and RIMP2/aug-cc-pVDZ levels of theory, and single point MP2/6-31+G* calculations at the DFT geometries. On the basis of the comparison with previous studies in solution and the calculated results, conformer A of 1 and 2 were assigned to a C6 conformer, while conformer B of 1 was assigned to a unique C8 structure with a weak intramolecular H-bond. The reasons for the preference for C6 over C8 structures and the presence of only two conformations in the jet-cooled spectrum are discussed in light of the predictions from calculations.

Single-Conformation Ultraviolet and Infrared Spectroscopy of Model Synthetic Foldamers: β-Peptides Ac-β3-hPhe-β3-hAla-NHMe and Ac-β3-hAla-β3-hPhe-NHMe

The conformational preferences and infrared and ultraviolet spectral signatures of two model beta-peptides, Ac-beta3-hPhe-beta3-hAla-NHMe (1) and Ac-beta3-hAla-beta3-hPhe-NHMe (2), have been explored under jet-cooled, isolated-molecule conditions. The mass-resolved, resonant two-photon ionization spectra of the two molecules were recorded in the region of the S0-S1 origin of the phenyl substituents (37,200-37,800 cm(-1)). UV-UV hole-burning spectroscopy was used to determine the ultraviolet spectral signatures of five conformational isomers of both 1 and 2. Transitions due to two conformers (labeled A and B) dominate the R2PI spectra of each molecule, while the other three are minor conformers (C-E) with transitions a factor of 3-5 smaller. Resonant ion-dip infrared spectroscopy was used to obtain single-conformation infrared spectra in the 3300-3700 cm(-1) region. The infrared spectra showed patterns of NH stretch transitions characteristic of the number and type of intramolecular H-bonds present in the beta-peptide backbone. For comparison with experiment, full optimizations of low-lying minima of both molecules were carried out at DFT B3LYP/6-31+G*, followed by single point MP2/6-31+G* and selected MP2/aug-cc-pVDZ calculations at the DFT optimized geometries. Calculated harmonic vibrational frequencies and infrared intensities for the amide NH stretch vibrations were used to determine the beta-peptide backbone structures for nine of the ten observed conformers. Conformers 1B, 1D, and 2A were assigned to double ring structures containing two C6 H-bonded rings (C6a/C6a), conformers 1A and 2B are C10 single H-bonded rings, conformers 1C and 2D are double ring structures composed of two C8 H-bonded rings (C8/C8), and conformers 1E and 2E are double ring/double acceptor structures in which two NH groups H-bond to the same C=O group, thereby weakening both H-bonds. Both 1E and 2E are tentatively assigned to C6/C8 double ring/double acceptor structures, although C8/C12 structures cannot be ruled out unequivocally. Finally, no firm conformational assignment has been made for conformer 2C whose unusual infrared spectrum contains one very strong H-bond with NH stretch frequency at 3309 cm(-1), a second H-bonded NH stretch fundamental of more typical value (3399 cm(-1)), and a third fundamental at 3440 cm(-1), below that typical of a branched-chain free NH. The single conformation spectra provide characteristic wavenumber ranges for the amide NH stretch fundamentals ascribed to C6 (3378-3415 cm(-1)), C8 (3339-3369 cm(-1)), and C10 (3381-3390 cm(-1)) H-bonded rings.

Molecular Rotors as Simple Models to Study Amide NH−Aromatic Interactions and Their Role in the Folding of Peptide-like Structures

The conformational behavior of designed macrocyclic naphthalenophanes (1a,b and 2a,b) derived from amino acids (Phe and Val) has been used for studying NH...pi interactions. The cycles having 16- and 17-membered rings showed a dynamic process within the NMR time scale, produced by the flipping of the aromatic naphthalene moiety with respect to the macrocyclic main plane. We used the temperature dependence of 1H NMR to obtain activation parameters of the energetic barrier for the process (variable temperature NMR and line shape analysis). The rate of the movement clearly depends on the macrocyclic ring size and, more interestingly, on the nature of the peptidomimetic side chain, the energetic barrier being higher for the compounds bearing aromatic side chains. A largely negative entropic contribution to the free energy of activation was observed, with clear differences due to the side chain nature. Molecular modeling studies suggest that the aromatic rings interact with intramolecularly H-bonded amide NH groups, protecting them from solvation and thus leading to a larger unfavorable activation entropy. This NH...pi interaction has been exploited for the preparation of new systems (1c and meso-1b) with designed conformational preferences, in which aromatic rings tend to fold over amide NH groups. Thus, these minimalistic molecular rotors have served us as simple model systems for the study of NH...pi interactions and their implication in the folding of peptide-like molecules.

Molecular structure of H-bonded complexes of N,N-diphenylformamidine studied by IR and NMR spectroscopy and quantum chemical calculations

The results of experimental studies and theoretical calculations of vibrational frequencies and structure of H-bonded associates of N,N-diphenylformamidine and its complexes with carboxylic acids and hydrogen chloride in solution are discussed. The IR and low temperature NMR spectra show the existence of equilibrium between s-trans-monomers and cyclic dimers, such as cyclic H-bonded complexes with carboxylic acids in solution. The complexes with weak acids have molecular structure. The interaction with strong acids and hydrogen chloride results in formation of H-bonded ionic pairs with proton transfer to the N atom of the base. The results of quantum chemical calculations confirm the formation of cyclic molecular complexes with two H-bonds NH…O C and OH…N at the interaction with weak carboxylic acids; the proton transfer along the OH…N bridge was found for the complexes with stronger proton donors. The vibrational frequencies and intensities were obtained also by a version of variational multidimensional anharmonic calculations of vibrational electrooptic parameters in space of normal coordinates. It was shown that this approach is more preferable for calculating the high-frequency XH stretch in systems where the corresponding normal mode is less characteristic and involves motions of many atoms.

Fourier Transform Infrared Spectrum of the Secondary Quinone Electron Acceptor QBin Photosystem II

Fourier transform infrared difference spectra upon single reduction of the secondary quinone electron acceptor Q(B) in photosystem II (PSII), without a contribution from the electron donor-side signals, were obtained for the first time using Mn-depleted PSII core complexes of the thermophilic cyanobacterium Thermosynechococcus elongatus. The Q(B)(-)/Q(B) difference spectrum exhibited a strong C...O stretching band of the semiquinone anion at 1480 cm(-)(1), the frequency higher by 2 cm(-)(1) than that of the corresponding band of Q(A)(-), in agreement with the previous S(2)Q(B)(-)/S(1)Q(B) spectrum of the PSII membranes of spinach [Zhang, H., Fischer, G., and Wydrzynski, T. (1998) Biochemistry 37, 5511-5517]. Also, several peaks originating from the Fermi resonance of coupled His modes with its strongly H-bonded NH vibration were observed in the 2900-2600 cm(-)(1) region, where the peak frequencies were higher by 7-24 cm(-)(1) compared with those of the Q(A)(-)/Q(A) spectrum. These frequency differences suggest that H-bond interactions of the CO groups, especially with a His side chain, are different between Q(B)(-) and Q(A)(-). Furthermore, a prominent positive peak was observed at 1745 cm(-)(1) in the C=O stretching region of COOH or ester groups in the Q(B)(-)/Q(B) spectrum. The peak frequency was unaffected by D(2)O substitution, indicating that this peak does not arise from a COOH group but probably from the 10a-ester C=O group of the pheophytin molecule adjacent to Q(B). The absence of protonation of carboxylic amino acids upon Q(B)(-) formation in contrast to the previous observation in the purple bacterium Rhodobacter sphaeroides suggests that the protonation mechanism of Q(B) in PSII is different from that of bacterial reaction centers.

Intramolecular Hydrogen Bonding in the S1(ππ*) Excited State of Anthranilic Acid and Salicylic Acid: TDDFT Calculation of Excited-State Geometries and Infrared Spectra

The equilibrium geometries and vibrational spectra of anthranilic acid (AA) and salicylic acid (SA) in the S1(ππ*) excited state have been determined with time-dependent density functional theory (TDDFT). A single minimum of the excited-state potential-energy surface, rather than separate amino/imino (enol/keto) minima, is found for AA and SA. A significant strengthening of the intramolecular hydrogen bond upon electronic excitation is predicted for both systems. The excited-state minimum corresponds to a shortening of the intramolecular hydrogen bond by 0.226 A (0.322 A) in AA (SA). The calculated 0−0 excitation energies are within 0.1 eV of the experimental values. An exceptionally large red shift of 1400 cm-1 and a strong mixing with H-chelate ring bending and stretching motions is predicted for the phenolic OH stretching vibration in the S1 state of salicylic acid. In anthranilic acid, a red shift of 500 cm-1 is obtained for the H-bonded amino NH stretching vibration, in excellent agreement with a rec...