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1.
Classical examples of supramolecular recognition units or synthons are the ones formed by hydrogen bonds. Here, we report the ubiquity of a S⋅⋅⋅O chalcogen bonded synthon observed in a series of supramolecular complexes of the amyotrophic lateral sclerosis drug riluzole. Although the potential of higher chalcogens such as Se and Te to form robust and directional chalcogen bonded motifs is known, intermolecular sulfur chalcogen bonding is considered to be weak owing to the lower polarizability of S atoms. Here, the robustness and electronic nature of a S⋅⋅⋅O chalcogen bonding non-classical synthon, and the origin of its exceptional directionality have been explored. Bond orders of the drug–coformer chalcogen bonding are found to be as high as one third of a single bond, and they are largely ionic in nature. The contribution of the S⋅⋅⋅O chalcogen bonded motifs to the lattice energies of a series of crystals from the Cambridge Structural Database has been analyzed, showing they can be indeed significant, especially in molecules devoid of strong hydrogen bond donor groups.  相似文献   

2.
Four conformers of the heterodimer o-anisic acid–formic acid, formed in a supersonic expansion, have been probed by Fourier transform microwave spectroscopy. Two of these forms have the typical double intermolecular hydrogen-bond cyclic structure. The other two show the o-anisic acid moiety bearing a trans-COOH arrangement supported by an intramolecular O−H⋅⋅⋅O bond to the neighbor methoxy group. In these conformers, formic acid interacts with o-anisic acid mainly through an intermolecular O−H⋅⋅⋅O hydrogen bond either to the O−H or to the C=O moieties, reinforced by other weak interactions. Surprisingly, the most abundant conformer in the supersonic expansion is the complex in which the o-anisic acid is in trans arrangement with the formic acid interacting with the O−H group. Such a trans-COOH arrangement in which the intramolecular hydrogen bond dominates over the usually observed double intermolecular hydrogen bond interaction has never been observed previously in an acid–acid dimer.  相似文献   

3.
The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O−H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.  相似文献   

4.
The properties of the intermolecular hydrogen bonds in the monoclinic (Form I) and the orthorhombic (Form II) polymorphs of paracetamol, C(8)H(9)NO(2), have been studied by single crystal polarized Raman spectroscopy (40 to 3700 cm(-1)) in a wide temperature range (5 K < T < 300 K) in relation to the dynamics of methyl-groups of the two forms. A detailed analysis of the temperature dependence of the wavenumbers, bandwidths and integral intensities of the spectral bands has revealed an essential difference between the two polymorphs in the strength and ordering of OH···O and NH···O hydrogen bonds. The compression of intermolecular hydrogen bonds is interrelated with crystal packing and the dynamics of methyl-groups. On structural compression of the orthorhombic polymorph on cooling, a compromise is to be sought between the shortening of OH···O and NH···O bonds, attractive CH···O and repulsive CH···H contacts in the crystal structure. As a result of a steric conflict at temperatures below 100 K, N-H···O hydrogen bonds become significantly disordered, and an extended intramolecular transition from the conformation "staggered" with respect to the C=O bond to the one "staggered" with respect to the NH bond is observed. In most of the studied crystals this transition was only about 60% complete even at 5 K, but in some of the crystals the orientation of all the methyl-groups became staggered with respect to the NH bond at low temperatures. This complete transition was coupled to a sharp shortening of the OH···O and NH···O hydrogen bonds at <100 K, the appearance of new additional positions of the protons in these H-bonds, and a slight strengthening of the C-HO bonds formed by methyl-groups. The same conformational transition has been observed also in the monoclinic polymorph at T < 80 K. The crystal packing in Form I prevents the O-H···O hydrogen bonds from adopting the optimum geometry, and they are significantly disordered at all the temperatures, especially at ≤200 K. The packing of molecules in Form I is also not favourable to form C-H···O hydrogen bonds involving methyl-groups. One can conclude from the comparison of diffraction and spectroscopic data that the higher stability of Form I results not from a larger strength of individual OH···O and NH···O hydrogen bonds, but is a cumulative effect: all the hydrogen bonds together stabilize the structure of the monoclinic polymorph more than that of the orthorhombic polymorph.  相似文献   

5.
A series of disubstituted benzamides related to the sterically hindered 2,6-dimethoxybenzamide drugs, such as remoxipride, are prepared. The structure-retention relationships for these compounds are studied on hydrocarbon stationary phases in various hydroorganic mobile phases. The 2,6-dimethoxybenzamide displays a very low capacity factor under these reversed-phase conditions, suggesting that steric crowding prevents the formation of an amide-methoxy N-H...O intramolecular hydrogen bond. The corresponding 2-hydroxy-6-methoxybenzamide shows a dramatic increase in affinity for the hydrocarbon stationary phase, which is characteristic of strong intramolecular hydrogen bonding in these compounds. These results suggest that the aromatic ring--carbonyl aqueous solution conformation is almost 90 degrees in amides like remoxipride and changes to coplanarity upon demethylation of one methoxy group.  相似文献   

6.
We studied the influence of hydrogen bonding on the fundamental and overtone bands of the OH-stretching vibration of each OH group in the intramolecularly hydrogen-bonded OH(I)::OH(II) pair in 1,2-, 1,3- and 1,4-diols. The hydrogen bonding between the two OH groups significantly increases in strength from the five-membered ring of a 1,2-diol to the seven-membered ring of a 1,4-diol. Although the hydrogen bonding does not affect the vibrational property of the OH(II) (or acceptor), it significantly influences the OH(I) (or donor). As the hydrogen bonding becomes stronger from a 1,2- to a 1,4-diol, the fundamental band of the OH-stretching shifts downwards by from about 50 to 140 cm(-1), and the overtone band markedly decreases in intensity, although the effect on the intensity and bandwidth of the fundamental band varies among 1,2-, 1,3- and 1,4-diols. The quantum-mechanically calculated normal frequencies of the acceptor and donor OH groups in the hydrogen-bonded ring are in good agreement with the observed frequencies. The calculated interatomic distance between the O of an acceptor OH and the H of a donor OH is the shortest for a 1,4-diol, which is consistent with the largest frequency shift caused by the hydrogen bonding.  相似文献   

7.
The synthesis of novel ortho-coumaric acid derivatives, with an amide group linked with an olefin moiety, which introduced photoinduced switching of the intramolecular hydrogen bonds is presented. An intramolecular OH...O=C hydrogen bond formed in a Z-phenol compound was switched to an intramolecular NH...O hydrogen bond in Z phenolate state via deprotonation. The pK(a) value of the Z-phenol derivative was lower than that of E-phenol, and a novel photocycle system involving protonation and deprotonation processes was achieved.  相似文献   

8.
We present a new and alternative interpretation of the structure of the IR vibrational mode (nu(OH) band) of pure water. The re-interpretation is based on the influence of the cooperative hydrogen bonding arising from a network of hydrogen bonds in the liquid. The nu(OH) band has six components that are dominated by differences in their O-H bond lengths but deviate from thermodynamically average values due to interactions with the hydrogen bond network. The physical origin of the structure in the nu(OH) band is directly related to the O-H bond length, and variations in this bond length are caused by the influence of the surrounding hydrogen-bonded network of water molecules.  相似文献   

9.
The characteristics of the intramolecular hydrogen bond (IMHB) for a series of 40 different enols of beta-diketones and their nitrogen counterparts have been systematically analyzed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. In some cases, two tautomers may exist which are interconnected by a hydrogen shift through the IMHB. In tautomer a the HB donor group (YH) is attached to the six-membered ring, while in tautomer b the HB acceptor (X) is the one that is attached to the six-membered ring. We found that changing an O to a N favors the a tautomer when the atom is endo and the contrary when it is exo, while the presence of a double bond favors the a tautomers. As expected, the OH group behaves as a better HB donor than the NH2 group and the C=NH group as a better HB acceptor than the C=O group, although the first effect clearly dominates. Accordingly, the expected IMHB strength follows the [donor, acceptor] trend: [OH, C=NH] > [OH, C=O] > [NH2, C=NH] > [NH2, C=O]. For all those compounds in which the functionality exhibiting the IMHB is unsaturated (I-type), the IMHB is much stronger than in their saturated counterparts (II-type). However, when the systems of the II-type subset, which are saturated, are constrained to have the HB donor and the HB acceptor lying in the same plane and at the same distance as in the corresponding unsaturated analogue, the IMHB is of similar or even larger strength. Hence, we conclude that, at least for this series of unsaturated compounds, the resonance-assisted hydrogen bond effect is not the primary reason behind the strength of their IMHBs, which is simply a consequence of the structure of the sigma-skeleton of the system that keeps the HB donor and the HB acceptor coplanar and closer to each other.  相似文献   

10.
The 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline scaffold is presented as a novel model system for the characterization of the weak NH⋅⋅⋅F hydrogen bonding (HB) interaction. In this scaffold, the aniline NH proton is forced into close proximity with the nearby fluorine (dH,F∼2.0 Å, ∠∼138°), and a through-space interaction is observed by NMR spectroscopy with couplings (1hJNH,F) of 19±1 Hz. A combination of experimental (NMR spectroscopy and X-ray crystallography) and theoretical methods (DFT calculations) were used for the characterization of this weak interaction. In particular, the effects of conformational rigidity and steric compression on coupling were investigated. This scaffold was used for the direct comparison of fluoride with methoxy as HB acceptors, and the susceptibility of the NH⋅⋅⋅F interaction to changes in electron distribution and resonance was probed by preparing a series of molecules with different electron-donating or -withdrawing groups in the positions para to the NH and F. The results support the idea that fluorine can act as a weak HB acceptor, and the HB strength can be modulated through additive and linear electronic substituent effects.  相似文献   

11.
Intermolecular hydrogen bonding competes with an intramolecular hydrogen bond when methanol binds to an alpha-hydroxyester. Disruption of the intramolecular OH...O=C contact in favour of a cooperative OH...OH...O=C sequence is evidenced by FTIR spectroscopy for the addition of methanol to the esters methyl glycolate, methyl lactate and methyl alpha-hydroxyisobutyrate in seeded supersonic jet expansions. Comparison of the OH stretching modes with quantum-chemical harmonic frequency calculations and 18O labelling of methanol unambiguously prove the insertion of methanol into the intramolecular hydrogen bond. This is in marked contrast to UV/IR hole burning studies of the homologous system methyl lactate: (+/-)-2-naphthyl-1-ethanol, where only addition complexes were found and the intramolecular hydrogen bond was conserved. This switch in hydrogen bond pattern from aliphatic to aromatic heterodimers is thought to reflect not only a kinetic propensity but also a thermodynamic preference for addition complexes when dispersion forces become more important in aromatic systems.  相似文献   

12.
Vibrational energy transfer (VET) of proteins at cell membrane plays critical roles in controlling the protein functionalities, but its detection is very challenging. By using a surface‐sensitive femtosecond time‐resolved sum‐frequency generation vibrational spectroscopy with infrared pump, the detection of the ultrafast VET in proteins at cell membrane has finally become possible. The vibrational relaxation time of the N−H groups is determined to be 1.70(±0.05) ps for the α‐helix located in the hydrophobic core of the lipid bilayer and 0.9(±0.05) ps for the membrane‐bound β‐sheet structure. The N−H groups with strong hydrogen bonding gain faster relaxation time. By pumping the amide A band and probing amide I band, the vibrational relaxation from N−H mode to C=O mode through two pathways (direct coupling and through intermediate states) is revealed. The ratio of the pathways depends on the NH⋅⋅⋅O=C hydrogen‐bonding strength. Strong hydrogen bonding favors the coupling through intermediate states.  相似文献   

13.
Extensive experimental and theoretical investigations are reported on the nature of resonance-assisted hydrogen bonding phenomenon (RAHB) and its influence on photophysical properties of the newly designed dyes differing in donor–acceptor properties, namely ethyl N-salicylideneglycinate ( 1 ), ethyl N-(5-methoxysalicylidene)glycinate ( 2 ), ethyl N-(5-bromosalicylidene)glycinate ( 3 ) and ethyl N-(5-nitrosalicylidene)glycinate ( 4 ). All compounds are thermochromic in the solid state and they contain a typical intramolecular O−H⋅⋅⋅N hydrogen bond formed between the hydroxyl hydrogen atom and the imine nitrogen atom, yielding the enol form in the solid state. It is unveiled, that the magnitude of RAHB effect fine tunes the strength of the O−H⋅⋅⋅N bonding and accordingly the relative populations of the enol, cis-keto and trans-keto forms leading to variation of the photophysical properties of 1 – 4 . It is determined, that the electron-withdrawing NO2 in 4 amplifies the most RAHB effect causing the breaking of the O−H⋅⋅⋅N hydrogen bond and accordingly formation of the dominant cis-keto isomer in both the solid state and EtOH. To this end, the UV/Vis spectra of 1 – 3 in EtOH revealed the exclusive presence of the enol form, while the prevalent contribution of the cis-keto form was found for 4 . Furthermore, only compound 4 is emissive in the solid state in ambient condition due to dual emission arising from the cis-keto* and trans-keto* forms, while 2 was found to be highly emissive in EtOH. It is revealed qualitatively and quantitatively, based on the ETS-NOCV charge and energy decomposition scheme and the EDDB population-based method, that RAHB is strongly a non-local phenomenon based on electrons pumping or sucking through both the π- and σ-channels, which accordingly exerts chemical bonding changes at both the phenyl ring and predominantly a distant O−H⋅⋅⋅N area.  相似文献   

14.
Amide oxygen co-ordination to a zinc(II) ion around a hydrogen bonding microenvironment is a common structural/functional feature of metalloproteases. We report two strategies to position hydrogen bonding groups in the proximity of a zinc(II)-bound amide oxygen, and we investigate their effect on the stability of the amide group. Polydentate tripodal ligands (6-R1-2-pyridylmethyl)-R2 (R1= NHCOtBu, R2= N(CH2-py-6-X)2 X = H L1, X = NH2, H L2, X = NH2 L3) form [(L)Zn]2+ cations (L =L1, 1; L2, 2; L3, 3) with intramolecular amide oxygen co-ordination (1-3), and intramolecular N-H...O=C(amide) hydrogen bonding (2, 3) rigidly fixed by the ligand framework. 1-3 undergo cleavage of the tert-butyl amide upon addition of Me4NOH.5H2O (1 equiv.) in methanol at 50(1) degrees C. Under these conditions the half-life, t(1/2), of the amide bond is 0.4 h for 1, 9 h for 2 and 320 h for 3. Mononuclear zinc(II) complexes of (6-NHCOtBu-2-pyridylmethyl)-R2(R2= N(CH2CH2)2S) L4 and chelating N2 ligands without hydrogen bonding groups (1,10-phenanthroline L5, 2-(aminomethyl)pyridine L6) as control compounds, and with an amino hydrogen bonding group (6-amino-2-(aminomethyl)pyridine L7) have been synthesised. Amide cleavage is in this case faster at the zinc(II) complex with the amino hydrogen bonding group. Thus, hydrogen bonding environments can both accelerate and slow down amide bond cleavage reactions at zinc(II) sites. Importantly, the magnitude of the effect exerted by the hydrogen bonding environments was found to be significant; 800-fold rate difference. This result highlights the importance of hydrogen bonding environments around metal centres in amide cleavage reactions, which may be relevant to the chemistry of natural metalloproteases and applicable to the design of more efficient artificial protein cleaving agents.  相似文献   

15.
Proton nuclear magnetic resonance chemical shifts and atom–atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─HOH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─HOH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─HOH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─HOH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.  相似文献   

16.
The crystal structures of N‐aryl‐1,2,3,4‐tetrahydro‐3,3‐dimethyl‐2,4‐quinolinediones bearing methoxy‐ ( 1 ), methyl‐ ( 2 ), and chloro‐ ( 3 ) substituents in 2′‐position of the phenyl ring have been determined by X‐ray crystal structure analysis. The heterocyclic ring in 1–3 adopts an envelope conformation, with the smallest ring puckering in the ortho‐chloro derivative 3 . The N‐aryl ring is almost perpendicular with respect to the quinoline‐2,4‐dione ring. The corresponding dihedral angle values are 83.2(1)°, 80.0(9)°, and 83.4(2)° in 1, 2 and 3 , respectively. The hydrogen bond of C H⋅⋅⋅O type joins the molecules of the ortho‐methoxy derivative 1 into dimers. The supramolecular structure also contains two C H⋅⋅⋅π interactions that link the hydrogen‐bonded dimers into sheets. In ortho‐methyl derivative 2 , one C H⋅⋅⋅π interaction generates infinite chains, whereas two C H⋅⋅⋅O hydrogen bonds and three C H⋅⋅⋅π interactions in the ortho‐chloro derivative 3 form three‐dimensional framework. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:325–331, 2008; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20436  相似文献   

17.
The title compound, C19H21N3O4S, crystallizes in the space group P2/c with two molecules in the asymmetric unit. The conformation of both molecules is very similar and is mainly determined by an intramolecular N—H...O hydrogen bond between a urea N atom and a sulfonyl O atom. The O and second N atom of the urea groups are involved in dimer formation via N—H...O hydrogen bonds. The intramolecular hydrogen‐bonding motif and conformation of the C—SO2—NH(C=O)—NH—C fragment are explored and compared using the Cambridge Structural Database and theoretical calculations. The crystal packing is characterized by π–π stacking between the 5‐cyanobenzene rings.  相似文献   

18.
The characteristics of intramolecular hydrogen bonds (IMHB) have been systematically analyzed for a series of 32 different enols of derivatives of cyclobutane, cyclobutene, and cyclobutadiene bearing oxygen and nitrogen functionalities, at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. In those cases where two tautomers (interconnected by a hydrogen shift through the IMHB) exist, tautomer a, in which the HB-donor group (YH) is attached to the four-membered ring, is less stable than tautomer b, in which is the HB-acceptor (X) is the one attached to the four-membered ring. As expected the OH group behaves as a better HB-donor than the NH(2) group and the C==NH group as a better HB-acceptor than the C==O group, although the first effect clearly dominates. Accordingly, the expected IMHB strength follows the [donor, acceptor] trend: [OH,C==NH]>[OH,C==O]>[NH(2),C==NH]>[NH(2),C==O]. Quite unexpectedly, in all those compounds in which the functionality exhibiting the IMHB is unsaturated, the IMHB is weaker than in their saturated counterparts, verifying that the primary effect on the strength of the IMHB is the structure of the sigma-skeleton of the system. In the conjugated systems investigated here, the severe constraints imposed by the four-membered ring force the HB donor and acceptor to be far apart and the IMHB is rather weak. These geometrical constraints are less severe for the saturated analogues and the IMHB becomes stronger, confirming that the characteristics of the sigma-skeleton, and not the resonance-assisted hydrogen bond (RAHB) phenomenon, are the primary contributors to the strength of the IMHB in conjugated compounds.  相似文献   

19.
Infrared absorptions for the matrix-isolated lead and tin hydroxides M(OH), M(OH)2 and M(OH)4 (M = Pb, Sn) were observed in laser-ablated metal atom reactions with H2O2 during condensation in excess argon. The major M(OH)2 product was also observed with H2 and O2 mixtures, which allowed the substitution of 18O2. The band assignments were confirmed by appropriate D2O2, D2, 16O18O, and 18O2 isotopic shifts. MP2 and B3LYP calculations were performed to obtain molecular structures and to reproduce the infrared spectra. The minimum energy structure found for M(OH)2 has C(s) symmetry and a weak intramolecular hydrogen bond. In experiments with Sn, HD, and O2, the internal D bond is favored over the H bond for Sn(OH)(OD). The Pb(OH)4 and Sn(OH)4 molecules are calculated to have S4 symmetry and substantial covalent character.  相似文献   

20.
Experimental evidence for intramolecular blue-shifting C-H...O hydrogen bonding is presented. Argon matrix-isolation infrared spectra of 1-methoxy-2-(dimethylamino)ethane exhibit a band at 3016.5 cm-1. Spectral behavior with annealing indicates that this band is assigned to the most stable conformer, trans-gauche-(trans|gauche'), with an intramolecular C-H...O hydrogen bond. Density functional calculations show that this band arises from the stretching vibration of the C-H bond participating in the formation of the C-H...O hydrogen bond. The C-H bond is shortened by 0.004 A, and the C-H stretching band is blue-shifted by at least 35 cm-1 on the formation of the hydrogen bond. The (C)H...O distance is calculated as 2.38 A, which is shorter than the corresponding van der Waals separation by 0.3 A.  相似文献   

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