Structure and matrix isolation infrared spectrum of formyl fluoride dimer: blue-shift of the C-H stretching frequency

Infrared spectroscopy (IR) of formyl fluoride (HCOF) dimer is studied in low-temperature argon and krypton matrixes. New IR absorptions, ca. 17 cm(-1) blue shifted from the monomer C-H stretching fundamental, are assigned to the HCOF dimer. The MP2/6-311++G calculations were utilized to define structures and harmonic frequencies of various HCOF dimers. Among the four optimized structures, the dimer having two C-H...O hydrogen bonds possesses strongest intermolecular bonding. The calculated harmonic frequencies of this dimer structure are shifted from the monomer similarly as observed in the experiment. Thus, we suggest that the experimentally observed blue shifted C-H bands belong to the dimer with two C-H...O hydrogen bonds. This observation includes the HCOF dimer to the class of hydrogen bonded complexes showing blue shift in their vibrational energies.     

Polar isomer of formic acid dimers formed in helium nanodroplets

The infrared spectrum of formic acid dimers in helium nanodroplets has been observed corresponding to excitation of the "free" OH and CH stretches. The experimental results are consistent with a polar acyclic structure for the dimer. The formation of this structure in helium, as opposed to the much more stable cyclic isomer with two O-H...O hydrogen bonds, is attributed to the unique growth conditions that exist in helium droplets, at a temperature of 0.37 K. Theoretical calculations are also reported to aid in the interpretation of the experimental results. At long range the intermolecular interaction between the two monomers is dominated by the dipole-dipole interaction, which favors the formation of a polar dimer. By following the minimum-energy path, the calculations predict the formation of an acyclic dimer having one O-H...O and one C-H...O contact. This structure corresponds to a local minimum on the potential energy surface and differs significantly from the structure observed in the gas phase.     

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.     

Transformations of griseofulvin in strong acidic conditions--crystal structures of 2'-demethylgriseofulvin and dimerized griseofulvin

The structure of griseofulvic acid, C16H15ClO6, at 100 K has orthorhombic (P2(1)2(1)2) symmetry. It is of interest with respect to biological activity. The structure displays intermolecular O-H...O, C-H...O hydrogen bonding as well as week C-H...pi and pi...pi interactions. In strong acidic conditions the griseofulvin undergoes dimerization. The structure of dimerized griseofulvin, C34H32C12O12 x C2H6O x H2O, at 100 K has monoclinic (P2(1)) symmetry. The molecule crystallized as a solvate with one ethanol and one water molecule. The dimeric molecules form intermolecular O-H...O hydrogen bonds to solvents molecules only but they interact via week C-H...O, C-H...pi, C-Cl...pi and pi...pi interactions with other dimerized molecules.     

Preparation, solid-state characterization, and computational study of a crown ether attached to a squaramide

[structure: see text] Crystals of a disecondary squaramide covalently linked to a crown ether presents a great variety of inter- and intramolecular nonbonded interactions including C-H/pi contacts, C-H...O and N-H...O hydrogen bonds, and pi-pi stacking between squaramide rings. Latter interaction, the stacking between squaramide rings, can be considered as an experimental evidence for the proposed aromaticity of squaramide when it is forming hydrogen bonds, either as acceptor or donor.     

Application of thin titanium/titanium oxide layers deposited on gold for infrared reflection absorption spectroscopy: structural studies of lipid bilayers

Ultrathin titanium layers when deposited on the surface of gold can be successfully applied for infrared reflection absorption spectroscopy (IRRAS) investigations. It was shown that the reflectivity, the phase shift, and the mean square electric field of the p- and s-polarized IR radiation in up to 20 nm thick titanium layers covered with a 3-4 nm thick layer of native oxide are comparable to those of the air/gold interface. The surface selection rule is fulfilled. Thus, qualitative and quantitative analysis of 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) bilayers transferred in liquid expanded (LE) and liquid condensed (LC) states can be performed. Differences are found in the hydration state and molecular arrangement of the two investigated bilayers. In the DMPC bilayer in the LE state, the C-N bond in the positively charged choline moiety is inclined by approximately 70 degrees toward the surface of the negatively charged titanium substrate. In the phosphate moiety, the in-plane vector of the O-P-O group makes a small angle of approximately 15 degrees to the surface normal. This open structure of the lipid molecule corresponds to the B crystal structure of the DMPC molecule and provides space for strong hydration of the polar headgroup. In the DMPC bilayer in the LC state, the intermolecular distances are reduced; the C-N bond of the choline group makes a smaller angle to the surface normal, and the in-plane vector of the O-P-O group in the phosphate moiety displays a larger tilt. The degree of hydration is reduced. The arrangement of the polar headgroup region corresponds to the A crystal structure of the DMPC molecule.     

The unexpected and large enhancement of the dipole moment in the 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) molecule upon crystallization: a new role of the intermolecular CH...O interactions.

The molecular dipole moment of the 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) molecule and its enhancement in the crystal was evaluated by periodic RHF ab initio computations. A discrete boundary partitioning of the electronic density that allows an unambiguous partitioning of the molecular space in the condensed phase was adopted. The resulting molecular dipole in the crystal compares favorably with the experimental value obtained by a multipolar analysis of single-crystal X-ray diffraction data recorded at 20 K, using a fuzzy boundary partitioning of the derived pseudoatom densities. We show that a large and highly significant molecular dipole enhancement may occur upon crystallization, despite the lack of a strongly hydrogen bonded environment in the crystal. The 23 unique C-H...O interactions which are formed upon packing of the DMACB molecule induce an increase in the molecular dipole (over 75%) that is comparable to or greater than that found in systems which are characterized by the stronger O-H...O and N-H...O hydrogen bonds. The DMACB molecule constitutes an excellent system for the study of C-H...O interactions in the condensed phase, since no other kind of competing hydrogen bonds is present in its crystal. A simple and qualitative model for the matrix contribution to the DMACB molecular dipole enhancement in the crystal is proposed. The formation of several weak C-H...O bonds is found to yield a small (about 0.2 e) net flux of electronic charge flowing from the hydrogens of the methyl groups to the carbonyl oxygen atoms. Despite the limited increase of the intramolecular charge transfer upon crystallization, a large molecular dipole enhancement occurs because the centroids of the positive and negative induced charges are quite far apart. This work highlights a new and important role of the C-H...O bond, besides those already known in the literature.     

Blue-shifted A-H stretching modes and cooperative hydrogen bonding. 1. Complexes of substituted formaldehyde with cyclic hydrogen fluoride and water clusters

The structures and vibrational spectra of the intermolecular complexes formed by insertion of substituted formaldehyde molecules HRCO (R = H, Li, F, Cl) into cyclic hydrogen fluoride and water clusters are studied at the MP2/aug-cc-pVTZ computational level. Depending on the nature of the substituent R, the cluster type, and its size, the C-H stretching modes of HRCO undergo large blue and partly red shifts, whereas all the F-H and O-H stretching modes of the conventional hydrogen bonds are strongly red-shifted. It is shown that (i) the mechanism of blue shifting can be explained within the concept of the negative intramolecular coupling between C-H and C=O bonds that is inherent to the HRCO monomers, (ii) the blue shifts also occur even if no hydrogen bond is formed, and (iii) variation of the acceptor X or the strength of the C-H...X hydrogen bond may either amplify the blue shift or cause a transition from blue shift to red shift. These findings are illustrated by means of intra- and intermolecular scans of the potential energy surfaces. The performance of the negative intramolecular coupling between C-H and C=O bonds of H(2)CO is interpreted in terms of the NBO analysis of the isolated H(2)CO molecule and H(2)CO interacting with (H2O)n and (HF)n clusters.     

Experimental evidence for intramolecular blue-shifting C-H...O hydrogen bonding by matrix-isolation infrared spectroscopy

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.     

Intramolecular hydrogen bonds in canonical 2'-deoxyribonucleotides: an atoms in molecules study

The molecular structure and relative stability of different conformers of isolated canonical 2'-deoxyribonucleotides thymidine-5'-phosphate (pdT), 2-deoxycytidine-5'-phosphate (pdC), 2-deoxyadenosine-5'-phosphate (pdA), and 2'-deoxyguanosine-5'-phosphate (pdG) were calculated using the B3LYP/6-31++G(d,p) level of theory. The results of the calculations reveal that, for all nucleotides except pdG, conformers with a syn orientation of the base do not correspond to a minimum on the potential energy surface. In the case of pdA and pdC, conformers with an orthogonal orientation of the nucleobase are located instead, north/syn conformers. These conformers as well as syn conformers of pdG are stabilized by intramolecular N-H...O hydrogen bonds. Analysis of the electron density distribution within the atoms in molecules theory reveals the presence of numerous C-H...O hydrogen bonds in the nucleotides. However, a more detailed consideration of the properties of these bonds demonstrates that many of them should be considered as strong attractive electrostatic interactions rather than true hydrogen bonds. True hydrogen bonds are represented mainly by C6/ C8-H...O5'/O-P in anti conformers and the N-H...O-P bonds in syn conformers. It is demonstrated that the values of ellipticity of the electron density at the bond critical point (BCP) and the distance between BCP and ring critical point are the most reliable indicators for determining the true intramolecular hydrogen bonds.     

Blue-shifting intramolecular C-H...O interactions

Two model systems, 3-methylacroleine and 3-(difluoromethyl)acroleine, are investigated computationally with respect to the character of the C-H...O interaction in their chelate-type (ZZ) conformers. By selecting the appropriate reference conformers, the C-H...O interaction is shown to result in the increase of the C-H stretching frequency (i.e., in the blue shift of the C-H stretching band). This is accompanied by the shortening of the C-H bond distance as compared to its values in reference molecules. Parallel to calculations of the C-H bond distance and stretching frequency, the energy contribution of the C-H...O interaction to the total energy (i.e., the energy associated with the C-H...O contact) is evaluated by using the methods proposed recently for the estimation of the energies of intramolecular hydrogen bonds. It is found that the C-H...O contact in the chelate-type forms of 3-methylacroleine and 3-(difluoromethyl)acroleine corresponds to the negative energy contribution and is repulsive. It is concluded that, despite the stability of the ZZ conformers of the two molecules and their deceptive structural shape, no hydrogen bond in the usual sense is formed between the C-H bond and the lone pair donor. The results are interpreted in terms of the steric compression, which leads to the dominance of the valence repulsion contribution in the C-H...O contact. This mechanism suggests that blue-shifting intramolecular interactions should not be that uncommon, although their recognition requires a careful consideration of the reference system.     

Oxa bowls: synthesis of new tetraoxa-cages and their C-H.O-mediated solid-state architecture

We have envisioned a new family of oxa-bowls, and a general approach to these entities has been proposed through polycyclic frameworks having two converging olefinic double bonds. Ozonolysis of such molecules was envisaged to give all-cis-tetraaldehyde functionality, which could undergo intramolecular cascade acetalization to oxa-bowls having C(2)(v )()symmetry. Homohypostrophene 16a and its functionalized derivative 16b and hypostrophene 17 on ozonolysis furnished the oxa-cages 22a, 22b, and 23, respectively. Single-crystal X-ray analysis of 22a and 23 showed an interesting network of C-H.O interactions mainly involving the nonacidic cycloalkane hydrogen atoms. The molecule 22a exhibits an interesting tapelike C-H.O hydrogen bonding motif in its crystal structure. On the other hand, the molecule 23 revealed an undulated ribbonlike C-H. O motif. The "chain of rings" pattern of C-H.O interactions in 23 has been observed for the first time in the solid-state structure of oxa-bowls.     

Improper hydrogen C-H...O bonds cause self-association of alpha, beta-enaminoketones containing fluorosubstituted alkyl groups.

Concentration- and temperature-dependent IR, NMR and dipole-moment studies on 4-N,N-dimethylamino-1,1,1-trifluoro-3-buten-2-one and two of its higher homologues showed that these compounds undergo reversible dimerization in nonpolar solvents. Antiparallel "closed" dimers are formed with a network of improper intermolecular C-H...O hydrogen bonds. Quantitative analysis of the 1H NMR data yielded delta H0 = -17.6 kJ mol-1 and delta S0 = -46.9 J deg-1 mol-1. The interactions observed are the strongest among those involving a C-H group reported so far. The complex described here is the first example of a cyclic complex stabilized by two improper C-H...O hydrogen bonds. The conclusions drawn from the solution and solid-state data were confirmed by ab initio calculations.     

Weak C-H...O and C-H...F-C hydrogen bonds in the oxirane-trifluoromethane dimer

The oxirane-trifluoromethane dimer generated in a supersonic expansion has been characterized by Fourier transform microwave spectroscopy. The rotational spectra of the parent species and of its two (13)C isotopomers in combination with ab initio calculations have been used to establish a C(s)() geometry for the dimer with the two monomers bound by one C-H.O and two C-H.F-C hydrogen bonds. An overall bonding energy of about 6.7 kJ/mol has been derived from the centrifugal distortion analysis. The lengths of the C-H.O and C-H.F hydrogen bonds, r(O.H) and r(F.H), are 2.37 and 2.68 A, respectively. The C-H.F-C interactions give rise to the HCF(3) internal rotation motion barrier of 0.55(1) kJ/mol, which causes the A-E splittings observed in the rotational spectra. The analysis of the structural and energetic features of the C-H.O and C-H.F-C interactions allows us to classify them as weak hydrogen bonds. Ab initio calculations predict these weak interactions to produce blue shifts in the C-H vibrational frequencies and shortenings of the C-H lengths.     

Crystal structures and 77Se NMR spectra of molybdenum(IV) areneselenolates having intramolecular NH...Se hydrogen bonds

Salts of the monooxomolybdenum(IV,V) areneselenolates having intramolecular NH...Se hydrogen bonds, [Mo(IV)O(Se-2-RCONHC6H4)4]2- (R = t-Bu, CH3, CF3) and [Mo(V)O(Se-2-t-BuCONHC6H4)4]-, were synthesized and characterized by 1H nuclear magnetic resonance (NMR), 77Se NMR, electron spin resonance (ESR), UV-visible spectra, X-ray analysis, and electrochemical measurements. 77Se-1H correlated spectroscopy (COSY) indicated a significant correlation between amide 1H and selenolate 77Se atoms through an NH...Se hydrogen bond with 1J(77Se-1H) = 5.4 Hz coupling. The hydrogen bonds contribute to the positive shift in the Mo(V)/Mo(IV) redox potential. In the crystal structure of (PPh4)2[Mo(IV)O(Se-2-CH3CONHC6H4)4], an NH...O=Mo hydrogen bond was found. Ab inito calculations support the presence of intramolecular NH...O=Mo and NH...Se hydrogen bonds.     

Two copper(II) complexes with 4-benzoylpyridine ligand: synthesis, crystal structure and luminescent properties

Two new copper(II) complexes Cu(NCS)2(4-Bzpy)2 (1) and Cu(NO3)2(4-Bzpy)4 (2) (4-Bzpy=4-benzoylpyridine) have been synthesized and characterized by IR, UV, elemental analysis and X-ray crystallography. Cu(II) atom has a square planar environment for 1 and an distorted octahedral environment for 2, respectively. In solid state there are C-H?π interactions and C-H?S hydrogen bonds between adjacent molecules in complex 1. The molecule of complex 2 is further connected by multiform π-π interactions, C-H?π interactions and C-H?O hydrogen bonds to form a three-dimensional supramolecular structure. The luminescent properties of the complexes 1 and 2 were both investigated in H2O solution and in solid state at room temperature, respectively.     

Structural, infrared, and density functional theory studies of N,N,N',N'-Tetramethylimidazolidinium dichloride: a model for cation-anion association of headgroups and counterions in the interfacial regions of gemini micelles

N,N,N',N'-Tetramethylimidazolidinium dichloride (1-Im-1 2Cl) has been studied as a model system for cation-anion interactions in the interfacial regions of gemini micelles by X-ray crystallography, density functional theory (DFT) calculations, and infrared spectroscopy. Single crystals of 1-Im-1 2Cl contain 1-Im-1 dications, whose five-membered rings adopt a distorted envelope conformation. Eight chloride anions surround each dication, two of which are cradled above and below the five-membered ring (apical) and six of which are dispersed about the periphery of the ring (equatorial). The cations and anions are linked in the solid state by an extensive network of weak C-H...Cl hydrogen bonds that involve all of the H atoms of the dication. The calculated (DFT at the 6-31+G(d) level) structure of the asymmetric unit, which consists of a dication and two apical chloride ions, closely resembles the equivalent unit in the crystal structure with respect to bond distances and angles, the conformation of the 1-Im-1 ring, and the nature and location of the C-H...Cl hydrogen bonds. The calculated IR spectrum predicts a number of absorptions in the 3000 cm(-1) region, assigned as C-H...Cl stretching modes, which are consistent with the presence of an intense band in the observed IR spectrum of the crystals. Over all, this study supports the notion that apical chloride ions interact more strongly with gemini surfactant headgroups by forming multiple hydrogen bonds in ion pairs of a type that cannot be present in the corresponding ion pairs of quaternary headgroups with counterions of single-chain surfactants.     

Conformational study of the 1,2,3-propanetriol (glycerol) in the channel of the aquaglyceroporin GlpF

The X-ray structure of the aquaglyceroporin GlpF protein refined by Fu et al. [D. Fu, A. Libson, L.J.W. Miercke, C. Weitzman, P. Nollert, J. Krucinski, R.M. Stroud, Science 290 (2000) 481--486.] shows three glycerol molecules co-crystallized inside the channel. The conformations of these molecules have been used to study the relationship between conformation, energy balance and hydration in the hope that it will provide insight into the molecular transport mechanism in the channel. Initially, the position of the hydrogen atoms of the glycerol molecule in the three conformations was established. As the glycerol molecule progressively loses its hydration waters in its transport pathway inside the channel, the nature of the glycerol bonds changes: the geometry of the alkyl backbone adapts to the available space while the progressive dehydration is partially compensated by the formation of intramolecular hydrogen bonds. The nature of these hydrogen bonds has been established by DFT calculation of the rotation barriers of the hydroxyl groups. Finally, the influence of the intramolecular hydrogen bonds on the conformation of the alkyl backbone has been established by quantum calculations of potential energy surfaces by semi-empirical quantum calculations PM3/Zindo.     

Blue-shifted A-H stretching frequencies in complexes with methanol: the decisive role of intramolecular coupling

The presence of a blue shift of A-H stretching frequencies in intermolecular complexes is directly related to the intramolecular coupling between A-H and vicinal A-X bonds in isolated molecules. The intramolecular coupling between vicinal bonds is the decisive parameter that determines whether a general molecule is a candidate for displaying blue-shifted A-H stretching frequencies in intermolecular complexes, with or without hydrogen bonding. The structures and vibrational spectra of dimeric complexes of methanol with H(2)O, HF, HCN, HNC, HOF, HNO, and HSN are investigated at the MP2/6-311++G(2d,2p) approach. Blue- and red-shifts of the methyl C-H stretches of methanol and the various other A-H stretching frequencies in the complexes can be predicted by normal coordinate analyses of methanol and the partner molecules. It is, hence, suggested that conventional normal coordinate analysis is the appropriate predictive tool to decide beforehand whether a given molecule is a promising candidate for the observation of blue shifts in intermolecular complexes.     

Molecular Recognition in Glycolaldehyde,the Simplest Sugar: Two Isolated Hydrogen Bonds Win Over One Cooperative Pair

Carbohydrates are used in nature as molecular recognition tools. Understanding their conformational behavior upon aggregation helps in rationalizing the way in which cells and bacteria use sugars to communicate. Here, the simplest α-hydroxy carbonyl compound, glycolaldehyde, was used as a model system. It was shown to form compact polar C₂-symmetric dimers with intermolecular O–H⋅⋅⋅O=C bonds, while sacrificing the corresponding intramolecular hydrogen bonds. Supersonic jet infrared (IR) and Raman spectra combined with high-level quantum chemical calculations provide a consistent picture for the preference over more typical hydrogen bond insertion and addition patterns. Experimental evidence for at least one metastable dimer is presented. A rotational spectroscopy investigation of these dimers is encouraged, also in view of astrophysical searches. The binding motif competition of aldehydic sugars might play a role in chirality recognition phenomena of more complex derivatives in the gas phase.