Origins of isotopomeric polymorphism

The complex formed between 4-methylpyridine and pentachlorophenol (4MPPCP) crystallises in a triclinic space group. If the same complex is synthesized from deuterated pentachlorophenol, it crystallizes in an entirely different monoclinic polymorph. Using solid-state NMR of samples synthesized with a full range of deuteration levels, crystallized from solution or the melt, and in the presence or absence of seeds, we have confirmed that the isotopomers indeed have different thermodynamically stable crystal structures. The roots of this phenomenon of isotopomeric polymorphism apparently lie in the differences in hydrogen bonding between the polymorphs. The triclinic form has a relatively short hydrogen bond. High-field solid-state NMR shows both the 1H chemical shift and the 2H electric quadrupole coupling of the hydrogen involved in the bond to be strongly temperature-dependent, indicating a low-lying excited state of the hydrogen bond longitudinal vibration. Inelastic neutron scattering of isotopomers of 4MPPCP has allowed us to identify the three orthogonal vibrational modes of the hydrogen in the hydrogen bond, at 29.7, 145, and 205 meV (240, 1168, and 1651 cm(-1)). The longitudinal mode is the lowest in energy, and it indicates a slightly asymmetric low-barrier double-well potential. Intrinsic to such potentials is a very small difference in zero-point energies (ZPEs) between the protonated and deuterated forms. As a contrast, the monoclinic form has a comparatively normal hydrogen bond, in which the proton and deuteron ZPEs should be different by approximately 500 cm(-1). A scenario can be envisaged where the triclinic protonated form is lower in energy than the monoclinic protonated form, but the triclinic deuterated form is higher in energy than the monoclinic deuterated form. This evidently accounts for the difference in relative stabilities of the two forms upon isotope substitution.     

Origins of isotopomeric polymorphism

The complex formed between 4-methylpyridine and pentachlorophenol (4MPPCP) crystallises in a triclinic space group. If the same complex is synthesized from deuterated pentachlorophenol, it crystallizes in an entirely different monoclinic polymorph. Using solid-state NMR of samples synthesized with a full range of deuteration levels, crystallized from solution or the melt, and in the presence or absence of seeds, we have confirmed that the isotopomers indeed have different thermodynamically stable crystal structures. The roots of this phenomenon of isotopomeric polymorphism apparently lie in the differences in hydrogen bonding between the polymorphs. The triclinic form has a relatively short hydrogen bond. High-field solid-state NMR shows both the ¹H chemical shift and the ²H electric quadrupole coupling of the hydrogen involved in the bond to be strongly temperature-dependent, indicating a low-lying excited state of the hydrogen bond longitudinal vibration. Inelastic neutron scattering of isotopomers of 4MPPCP has allowed us to identify the three orthogonal vibrational modes of the hydrogen in the hydrogen bond, at 29.7, 145, and 205 meV (240, 1168, and 1651 cm^?1). The longitudinal mode is the lowest in energy, and it indicates a slightly asymmetric low-barrier double-well potential. Intrinsic to such potentials is a very small difference in zero-point energies (ZPEs) between the protonated and deuterated forms. As a contrast, the monoclinic form has a comparatively normal hydrogen bond, in which the proton and deuteron ZPEs should be different by approximately 500 cm^?1. A scenario can be envisaged where the triclinic protonated form is lower in energy than the monoclinic protonated form, but the triclinic deuterated form is higher in energy than the monoclinic deuterated form. This evidently accounts for the difference in relative stabilities of the two forms upon isotope substitution.     

Time-dependent density functional theory study on excited state intramolecular proton transfer of 3-hydroxy-2-(pyridin-2-yl)-4H-chromen-4-one

The time-dependent density functional theory (TDDFT) method was carried out to investigate the excited state intramolecular proton transfer (ESIPT) process of 3-hydroxy-2-(pyridin-2-yl)-4H-chromen-4-one (1a). 1a has two tautomeric forms: one is 1a(O), which is induced by intramolecular hydrogen bond O-H?O=C, and the other one is 1a(N), which is caused by intramolecular hydrogen bond O-H?N. From excited state to tautomer excited state coming from ESIPT, the hydroxyl hydrogen breaks away and the dissociated hydrogen adsorbed on pyridinic nitrogen or carbonyl oxygen formed new intramolecular HB and the corresponding bond length and bond angle varied greatly. In comparison, a similar process of proton transfer for 1a(N)H⁺ protonated 1a(N) from ground state to excited state was obtained. This detailed proton transfer mechanism was provided by molecular orbitals analysis and it may be applied to molecular switch and organic Lewis acid/base. We investigated the excited state proton transfer mechanism of the four molecules through the theoretical method for the first time and gave unambiguous geometry of excited state.     

花二酸酐与嘧啶衍生物的氢键组装(英文)

用半经验AM1方法对苝二酸酐与嘧啶衍生物的1∶1及1∶2氢键复合物进行理论研究,表明随着氢键数目增多,弱相互作用能变大,主体上的供电基和客体上的吸电基有利于氢键相互作用,氢键导致电子从主体流向客体。用INDO／SCI方法计算配合物的电子光谱,表明其长波吸收峰与主体相比发生兰移,各配合物的长波吸收峰位置相差不大,与实验一致。讨论吸收峰兰移的原因并对电子跃迁进行理论指认,同时得到了配合物的双质子转移势能曲线,给出了相对于N-H键的过渡态和活化能。     

苝二酸酐与嘧啶衍生物的氢键组装

用半经验AM1方法对苝二酸酐与嘧啶衍生物的1:1及1:2氢键复合物进行理论研究,表明随着氢键数目增多,弱相互作用能变大,主体上的供电基和客体上的吸电基有利于氢键相互作用,氢键导致电子从主体流向客体.用INDO/SCI方法计算配合物的电子光谱,表明其长波吸收峰与主体相比发生兰移,各配合物的长波吸收峰位置相差不大,与实验一致.讨论吸收峰兰移的原因并对电子跃迁进行理论指认,同时得到了配合物的双质子转移势能曲线,给出了相对于N-H键的过渡态和活化能.     

The antioxidant activity of 4‐hydroxycoumarin derivatives and some sulfured analogs

In this work, the relationship between the structure and the radical scavenging activity of seven hydroxycoumarins and their sulfured analogs was investigated for the first time by density functional theory calculation in the gas phase, benzene, and water. Our investigation includes hydrogen atom transfer, single‐electron transfer–proton transfer, and sequential proton loss electron transfer mechanisms. The results revealed that the bond dissociation enthalpy values of sulfured coumarins were lower than those of hydroxylated analogs. The obtained results were in a good agreement with the experimental results. The hydrogen atom transfer mechanism is dominant in both benzene and vacuum. The sequential proton loss electron transfer mechanism represents the most thermodynamically preferred reaction pathway in water. However, single‐electron transfer–proton transfer mechanism is not the most preferred one in all media. Finally, this work contributes to the understanding of the pharmacological activity of the compounds studied. Copyright © 2015 John Wiley & Sons, Ltd.     

Investigation of structural changes related to temperature: An understanding of H-bond based proton transfer in 4(5)-vinylimidazole and acrylic acid copolymer membrane

An attempt to understand how proton transfer proceeds in poly (acrylic acid-co-4(5)-vinylimidazole) has been carried out based on the temperature dependent characterization techniques, i.e., Fourier transform infrared spectroscopy (FTIR), wide angle X-ray diffraction (WAXD), Raman spectroscopy, including the atomic distance calculations. Systematical studies are achieved from a series of poly (acrylic acid-co-4(5)-vinylimidazole) with different acrylic acid content. When the copolymer is almost an ideal in equimolar ratio of an alternating structure, the hydrogen bond between carboxylic acid and imidazole is maintained and initiates the proton conductivity even at 120 °C. Whereas when the copolymer is carboxylic acid rich, the dehydration to form anhydride proceeds resulting in the decrease in proton conductivity at high temperature. The radial distribution function (RDF) calculated from the WAXD pattern shows that the inter-atomic distances reflect how the increase in temperature induces a favorable packing structure under the hydrogen bond network and the chain mobility to enhance the proton transfer at high temperature, especially in the case of the copolymer with an ideal alternating structure.     

The photochemistry of the self‐healing chromophore Disperse Orange 11

Recent interest in the self‐healing ability of the laser dye 1‐amino‐2‐methylanthraquinone, Disperse Orange 11, has lead us to investigate the possible alternative mechanisms of action, either intramolecular proton transfer (PT) or twisted intramolecular charge transfer (TICT) formation. AMPAC semiempirical PM3 CI (all single excited configurations) potential energy surfaces searches have been conducted with either reaction mechanism. Based purely on the potential energy surface results, no state, S0, T1, or S1, seems especially likely to be kinetically favorable for PT. The T1 state is favorable thermodynamically for PT. However, the S1 state TICT reaction is both thermodynamically favorable and kinetically preferred over all PT reactions. There is also a favorable T1 TICT reaction, but much slower kinetically on the triplet surface than S1 TICT. The Wentzel–Kramers–Brillouin (WKB) method has been used to ascertain proton tunneling contributions to PT. Even with proton tunneling, S1 TICT is still more highly favored, though proton tunneling could make the T1 PT reaction competitive depending on the rate of intersystem crossing. We also examine spectroscopic properties of PT transfer and TICT reaction path entities in comparison with published experimental evidence. However, this comparison leads to ambiguous findings that suggest that electronic spectral properties alone will not fully clarify the mechanism. Overall, results suggest that the TICT mechanism is the most likely for optical damage and self‐repair for Disperse Orange 11, and might be considered for the damage and repair mechanisms for other organic solid state laser materials. Copyright © 2012 John Wiley & Sons, Ltd.     

A quantum chemical study on the OH radical quenching by natural antioxidant fisetin

In this work, the antioxidant ability of fisetin was explored toward hydroxyl (?OH) radical in aqueous and lipid solution using density functional level of theory. Different reaction mechanisms have been studied: hydrogen atom transfer, single electron transfer followed by proton transfer, and radical adduct formation, and sequential proton loss electron transfer. Rate constants for all possible reaction sites have been calculated using conventional transition state theory in conjunction with the Collins‐Kimball theory. Branching ratios for the different channels of reaction are reported for the first time. Results show that the reactivity of fisetin toward hydroxyl (^?OH) radical takes place almost exclusively by radical adduct formation regardless of the polarity of the environment. Also, the single‐electron transfer process seems to be thermodynamically unfavorable in both media.     

A DFT study on the structure and radical scavenging activity of newly synthesized hydroxychalcones

Quantum‐chemical computations based on the density functional theory have been employed to study the relation between the structure and the radical scavenging activity of six newly synthesized hydroxychalcones. The three main working mechanisms, hydrogen atom transfer (HAT), stepwise electron‐transfer‐proton‐transfer, and sequential‐proton‐loss‐electron‐transfer (SPLET), were investigated, and the O–H bond dissociation enthalpy, ionization potential, proton dissociation enthalpy, and electron transfer energy parameters were computed in the gas phase and in solvents using PCM model. The geometry structure, radical, electron character, and the frontier molecular orbital were analyzed to explore the key factors that influence the radical scavenging activity of the hydroxychalcones. Results indicated that 3,4‐dihydroxychalcone (6) possessing the catechol functionality is expected to be more efficient hydrogen atom and proton donor than others. The theoretical results confirm the important role of the B‐ring and shed light on the role of the o‐dihydroxy (catechol) moiety in the antioxidant properties of hydroxychalcones. In addition, the calculated results are in good agreement with experimental values. It was found that HAT is the most favored mechanism for explaining the radical‐scavenger activity of hydroxychalcone in the gas phase, whereas SPLET mechanism is thermodynamically preferred pathway in aqueous solutions. Copyright © 2012 John Wiley & Sons, Ltd.     

The effect of benzo‐annelation on intermolecular hydrogen bond and proton transfer of 2‐methyl‐3‐hydroxy‐4(1H)‐quinolone in methanol: A TD‐DFT study

Excited‐state intermolecular or intramolecular proton transfer (ESIPT) reaction has important potential applications in biological probes. In this paper, the effect of benzo‐annelation on intermolecular hydrogen bond and proton transfer reaction of the 2‐methyl‐3‐hydroxy‐4(1H)‐quinolone (MQ) dye in methanol solvent is investigated by the density functional theory and time‐dependent density functional theory approaches. Both the primary structure parameters and infrared vibrational spectra analysis of MQ and its benzo‐analogue 2‐methyl‐3‐hydroxy‐4(1H)‐benzo‐quinolone (MBQ) show that the intermolecular hydrogen bond O₁―H₂?O₃ significantly strengthens in the excited state, whereas another intermolecular hydrogen bond O₃―H₄?O₅ weakens slightly. Simulated electron absorption and fluorescence spectra are agreement with the experimental data. The noncovalent interaction analysis displays that the intermolecular hydrogen bonds of MQ are obviously stronger than that of MBQ. Additionally, the energy profile analysis via the proton transfer reaction pathway illustrates that the ESIPT reaction of MBQ is relatively harder than that of MQ. Therefore, the effect of benzo‐annelation of the MQ dye weakens the intermolecular hydrogen bond and relatively inhibits the proton transfer reaction.     

Structure and spectral-luminescent properties of 6-isoxazolyl-7-hydroxycoumarins

We have studied the particular features of the spectral and fluorescent properties of 6-isoxazolyl-7-hydroxycoumarin and its 7-methoxy-substituted analog in aprotic and proton-donor solvents of different polarity. Changes in the electron charge and bond orders in the ground and first excited states have been analyzed by the ab initio DFT and TDDFT quantum-chemical methods with the B3LYP/6–31G(d,p) basis set. Based on this analysis, we have analyzed anomalously high Stokes shifts, the shape of vibronic bands, and the fluorescence ability of these compounds in aprotic solvents. It has been found that the fluorescence spectra of hetaryl-substituted 7-hydroxycoumarin, in contrast with its absorption spectra in motional, DMSO, basic and acidic solutions, strongly differ from the fluorescence spectra of its 7-metoxy analog. We show that this is related to the proton detachment and transfer in the neutral form of 7-hydroxycoumarin upon photoexcitation with the possible formation of anion or tautomer depending on the pH of the medium.     

Theoretical mechanistic studies on the degradation of alizarin yellow R initiated by hydroxyl radical

The degradation of azo dyes has attracted many research efforts not only due to the resulting environmental problems but also because the azo compounds with various substituents may show different degradation mechanism. It has been computationally found here, for the first time, that the HO? initiated cleavages of C–N and N–N bonds of alizarin yellow R with carboxyl group are kinetically competitive. In view of the formation of HO? adducts, the C–N and N–N bond cleavages of the hydrazone tautomer of alizarin yellow R are also kinetically competitive, but the former is more thermodynamically favorable. This result is different from that previously reported for the hydrozone tautomers of Acid Orange 7 and Acid Orange 8 containing hydroxyl and azo groups in neighboring positions, which are favorable to follow C–N bond cleavage mechanism both kinetically and thermodynamically. The decarboxylation occurs via an attack of HO? to the benzene ring carbon connecting to the carboxyl group rather than a direct attack of HO? to the carboxyl carbon atom. The anion form has higher reactivity than the neutral form in all of the reactions investigated. In addition, a water molecule as a proton relay reagent could significantly reduce the energy barrier for the N–N bond cleavage of alizarin yellow R. Copyright © 2014 John Wiley & Sons, Ltd.     

The ESI CAD fragmentations of protonated 2,4,6-tris(benzylamino)- and tris(benzyloxy)-1,3,5-triazines involve benzyl-benzyl interactions: a DFT study

The electrospray ionization collisionally activated dissociation (CAD) mass spectra of protonated 2,4,6-tris(benzylamino)-1,3,5-triazine (1) and 2,4,6-tris(benzyloxy)-1,3,5-triazine (6) show abundant product ion of m/z 181 (C(14) H(13)(+)). The likely structure for C(14) H(13)(+) is α-[2-methylphenyl]benzyl cation, indicating that one of the benzyl groups must migrate to another prior to dissociation of the protonated molecule. The collision energy is high for the 'N' analog (1) but low for the 'O' analog (6) indicating that the fragmentation processes of 1 requires high energy. The other major fragmentations are [M?+?H-toluene](+) and [M?+?H-benzene](+) for compounds 1 and 6, respectively. The protonated 2,4,6-tris(4-methylbenzylamino)-1,3,5-triazine (4) exhibits competitive eliminations of p-xylene and 3,6-dimethylenecyclohexa-1,4-diene. Moreover, protonated 2,4,6-tris(1-phenylethylamino)-1,3,5-triazine (5) dissociates via three successive losses of styrene. Density functional theory (DFT) calculations indicate that an ion/neutral complex (INC) between benzyl cation and the rest of the molecule is unstable, but the protonated molecules of 1 and 6 rearrange to an intermediate by the migration of a benzyl group to the ring 'N'. Subsequent shift of a second benzyl group generates an INC for the protonated molecule of 1 and its product ions can be explained from this intermediate. The shift of a second benzyl group to the ring carbon of the first benzyl group followed by an H-shift from ring carbon to 'O' generates the key intermediate for the formation of the ion of m/z 181 from the protonated molecule of 6. The proposed mechanisms are supported by high resolution mass spectrometry data, deuterium-labeling and CAD experiments combined with DFT calculations.     

Adherence of packing defects in soluble proteins

For protein structure to prevail in water, its backbone hydrogen bonds must be shielded from water attack, requiring a cluster of "wrapping" nonpolar groups. Thus, underwrapped regions are adhesive, as exogenous removal of surrounding water becomes thermodynamically favorable. Here we measure the average adhesive force exerted by an underwrapped hydrogen bond on a test hydrophobe and thus define a new interactivity constant.     

H bonding of substituted pyridines on silica

The infrared spectra of a series of substituted pyridines which were adsorbed on silica have been obtained. A linear correlation is obtained between the wavenumber shift of the OH stretching fundamental of the surface hydroxyl groups towards lower wavenumber and the Hammett polar substituent parameter of the adsorbate. Deviations are only observed for tert.-butyl substituents in ortho-position and for ortho-substituents which render a dual interaction with neighbouring OH groups possible. The optical density of an IR continuous absorption is a function of the proton affinity of the adsorbate and it can be explained by assuming the formation of protonated adsorbed species which exhibit symmetrical NH⁺… N bond.     

Fluorescence quenching of betacarboline (9H-pyrido[3,4-b]indole) induced by intermolecular hydrogen bonding with pyridines

The influence of the hydrogen bond acceptor properties of pyridine derivatives on the fluorescence quenching mechanism of the betacarboline (9H-pyrido[3,4-b]indole) (BC) has been investigated. Absorption measurements suggest the sequential formation of two BC-pyridine hydrogen-bonded complexes: a covalent hydrogen-bonded complex (HBC) and its proton transfer tautomer (PTC). Steady-state and time-resolved fluorescence measurements reveal that the BC fluorescence quenching has static and dynamic components due to the ground and the excited state formation of the very weakly fluorescent PTC. Since the excited state HBC formation is a diffusion-controlled process, the efficiency of dynamic quenching is mainly determined by the relative magnitudes of the HBC backward reaction and the PTC formation rate constants.     

Far-Infrared Investigations of Hydrogen Bonded Complexes between Phenol and Substituted Pyridines

As known, the hydrogen bond can be described as an interaction between a proton-donor group (A-H) and a proton–acceptor group (B) with the formation of a complex of the type (A-H··B).     

The strong OHO hydrogen bond. How much covalency?

In the strong OHO hydrogen bond of the phosphoric acid–urea 1?:?1 complex the proton shifts gradually with temperature from the donor towards the acceptor atom, passing through the center of the hydrogen bond at around 315?K. The AIM parameters were evaluated for the published neutron structures at different temperatures. The values of the electron density, its Laplacian, and the energy densities at both the critical points between the proton and the oxygen atoms in the OHO hydrogen bond were correlated with the OH and HO distances. Changes in the AIM parameters of the strong hydrogen bond were compared with those of the weak NHO bond in this complex.