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1.
Ab initio calculations at the second-order M?ller-Plesset perturbation theoretic level have been carried out to study the solvation of protonated water by phenol molecules. The results show that in addition to classical O-H...O hydrogen bonds, C-H...O, pi...H-O, and pi...H-C bonds are also formed, thus stabilizing the H3O+(C(6)H(5)OH)3 complex.  相似文献   

2.
The T-shaped host molecule 4,4-bis(4'-hydroxyphenyl)cyclohexanone (1) has an equatorial phenol group and a cyclohexanone group along the arms and an axial phenol ring as the stem. The equatorial phenyl ring adopts a "shut" or "open" conformation, like a windowpane, depending on the size of the guest (phenol or o/m-cresol), for the rectangular voids of the hydrogen-bonded ladder host framework. The adaptable cavity of host 1 expands to 11x15-18 A through the inclusion of water with the larger cresol and halophenol guests (o-cresol, m-cresol, o-chlorophenol, and m-bromophenol) compared with a size of 10x13 A for phenol and aniline inclusion. The ladder host framework of 1 is chiral (P2(1)) with phenol, whereas the inclusion of isosteric o- and m-fluorophenol results in a novel polar brick-wall assembly (7x11 A voids) as a result of auxiliary C-H...F interactions. The conformational flexibility of strong O-H...O hydrogen-bonding groups (host 1, phenol guest), the role of guest size (phenol versus cresol), and weak but specific intermolecular interactions (herringbone T-motif, C-H...F interactions) drive the crystallization of T-host 1 towards 1D ladder and 2D brick-wall structures, that is, supramolecular isomerism. Host 1 exhibits selectivity for the inclusion of aniline in preference to phenol as confirmed by X-ray diffraction, 1H NMR spectroscopy, and thermogravimetry-infrared (TG-IR) analysis. The T(onset) value (140 degrees C) of aniline in the TGA is higher than those of phenol and the higher-boiling cresol guests (T(onset)=90-110 degrees C) because the former structure has more O-H...N/N-H...O hydrogen bonds than the clathrate of 1 with phenol which has O-H...O hydrogen bonds. Guest-binding selectivity for same-sized phenol/aniline molecules as a result of differences in hydrogen-bonding motifs is a notable property of host 1. Host-guest clathrates of 1 provide an example of spontaneous chirality evolution during crystallization and a two-in-one host-guest crystal (phenol and aniline), and show how weak C-H...F interactions (o- and m-fluorophenol) can change the molecular arrangement in strongly hydrogen-bonded crystal structures.  相似文献   

3.
A homologous series of bis-diphenylphosphine oxides (C6H5)2PO(CH2)(n)PO(C6H5)2 (with n = 2-8; denoted 2-8] have been investigated to explore the effects of a range of competing and cooperative intermolecular and intramolecular interactions on the structural properties in the solid state. The important factors influencing the structural properties include intramolecular aspects such as the conformation of the aliphatic chain and the intramolecular interaction between the two P=O dipoles in the molecule, and intermolecular aspects such as long-range electrostatic interactions (dominated by the arrangement of the P=O dipoles), C-H...O interactions, C-H...pi interactions and pi...pi interactions. Compounds 3 and 5 could be crystallized only as solvate co-crystals (3 water and 5 x (toluene)2], whereas the crystal structures of all the other compounds contain only the bis-diphenylphosphine oxide molecule. The crystal structures have been determined from single-crystal X-ray diffraction data, with the exception of 7 (which has been determined here from powder X-ray diffraction data) and 4 (which was known previously). The compounds with even n represent a systematic structural series, exhibiting characteristic, essentially linear P=O...P=O...P=O dipolar arrays, together with C-H...O and C-H...pi interactions. For the compounds with odd n, on the other hand, uniform structural behaviour is not observed across the series, although certain aspects of these crystal structures contribute in a general sense to our understanding of the structural properties of bis-diphenylphosphine oxides. Importantly, for the compounds with odd n, there is "frustration" with regard to the molecular conformation, as the preferred all-anti conformation of the aliphatic chain gives rise to an unfavourable parallel alignment of the two P=O dipoles within the molecule. Clearly the importance of avoiding a parallel alignment of the P=O dipoles becomes greater as n decreases. Local structural aspects (investigated by high-resolution solid-state 31P NMR spectroscopy) and thermal properties of the bis-diphenylphosphine oxide materials are also reported.  相似文献   

4.
The title compound, C31H37NO4S [systematic name: (R)-tert-butyl-2-[(tert-butoxycarbonyl)amino]-3-(tritylsulfanyl)propanoate] is an L-cysteine derivative with three functions: NH2, COOH and SH, blocked by protecting groups tert-butoxycarbonyl, tert-butyl and trityl, respectively. The main chain of the molecule adopts the extended, nearly all-trans C5 conformation with the intramolecular N-H...O=C hydrogen bond. The urethane group is not involved in any intermolecular hydrogen bonding. Only weak intermolecular hydrogen bonds and hydrophobic contacts are observed in the crystal structure. These are C-H...O hydrogen bonds and CH/pi interactions with donor...acceptor distances, C...O ca. 3.5 A and C...C ca. 3.7 A, respectively. The first type of interaction links phenyl H-atoms and carbonyl groups. The second type of interaction is formed between a methyl group of the tert-butyl fragment and a trityl phenyl ring. The resulting molecular conformation in the crystal is very close to an ab initio minimum energy conformer of the isolated molecule. The extended C5 conformation of the main peptide chain is the same and there is slight discrepancy in the disposition of trityl phenyl rings. Their small dislocation creates the possibility of forming the entire network above of extensive, specific, weak intermolecular interactions; these constrain the molecule and permit it to retain the minimum energy C5 conformation of its main chain in the solid state. In contrast, in n-hexane solution, where such specific interactions cannot occur, only a small population of the molecules adopts the extended C5 conformation.  相似文献   

5.
The MP2 method and the Pople-style basis sets 6-311++G(d,p), 6-311++G(2df,2pd), and 6-311++G(3df,3pd) were used to perform calculations on H3O+...C2H2 and C2H3+...C2H2 complexes and related species. Hydrogen bonds existing for the analyzed complexes were investigated as well as related pi-H...O --> pi...H-O and pi-H...pi --> pi...H-pi proton-transfer processes. For some of the complexes analyzed the multicenter pi-H interaction possessing the properties of a covalent bond acts as a proton donor; more generally it is classified as the Lewis acid. The quantum theory of "atoms in molecules" (QTAIM) was also applied to deepen the nature of these interactions in terms of characteristics of bond critical points. The pi-H...O, O-H...pi, and pi-H...pi interactions analyzed here may be classified as hydrogen bonds since their characteristics are the same as or at least similar to those of typical hydrogen bonds. H...pi interactions are common in crystal structures of organic and organometallic compounds. The analyses performed here show a continuum of such interactions since there are H...pi contacts possessing the characteristics of weak intermolecular interactions on the one hand and pi-H multicenter covalent bonds on the other. Ab initio and QTAIM results support the latter statements.  相似文献   

6.
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.  相似文献   

7.
A charge density study of crystalline 1-(4-fluorophenyl)-3,6,6-trimethyl-2-phenyl-1,5,6,7-tetrahydro-4H-indol-4-one (A) and 1-(4-fluorophenyl)-6-methoxy-2-phenyl-1,2,3,4-tetrahydroisoquinoline (B) has been carried out using high-resolution X-ray diffraction data collected at 113(2) K. Weak intermolecular interactions of the type C-H...O, C-H...pi, and pi...pi hold the molecules together in the crystal lattice along with interactions of the type C-H...F and unusual C-F...F-C examined via charge density analysis. The topological features are evaluated in terms of Bader's theory of atoms in molecules through the first four criteria of Koch and Popelier. The C-F...F-C contact is observed to be across the center of symmetry in B and not in A, and further, this interaction appears to possess a certain correlation with the electron density properties at the critical point which suggests that such an interaction fits into the hierarchy of weak interactions.  相似文献   

8.
The binary complexes of water with styrene and fluorostyrene were investigated using LIF and FDIR spectroscopic techniques. The difference in the shifts of S 1 <-- S 0 electronic transitions clearly points out the disparity in the intermolecular structures of these two binary complexes. The FDIR spectra in the O-H stretching region indicate that water is a hydrogen bond donor in both complexes. The formation of a single O-H...pi hydrogen-bonded complex with styrene and an in-plane complex with fluorostyrene was inferred based on the analysis of the FDIR spectra in combination with ab initio calculations. The in-plane complex with fluorostyrene is characterized by the presence of O-H...F and C-H...O hydrogen bonds, leading to formation of a stable six-membered ring. The synergistic effect of O-H...F and C-H...O hydrogen bonds overwhelms the O-H...pi interaction in fluorostyrene-water complexes.  相似文献   

9.
The calculated structures of furan as a monomer, a dimer that was isolated from the crystal structure, and the full crystal structure have been thoroughly investigated by a combination of density functional theory (DFT) calculations and inelastic neutron scattering (INS) measurements. To improve our understanding of the nature and magnitude of the intermolecular interactions in the solid, the atoms in molecules (AIM) theory has been applied to the dimer and a cluster of eight monomers. After a careful topological study of the theoretical charge density and of its Laplacian, we have established the existence of C-H...pi, C-H...O, and H...H interactions between adjacent molecules in solid furan. The electron distribution has also been analyzed by performing natural bond orbital (NBO) calculations for the monomer and a H-bonded dimer. When the hydrogen bond is established between two adjacent furan rings, some electron charge is transferred from the pi electronic system of one furan ring to the other molecule in the dimer. This result provides a model of the interaction between end groups of neighboring chains of polyfuran and could be applicable to other conjugated polymers where the pi system is responsible for their conducting properties. To determine how the intermolecular bonds in the solid affect the vibrational dynamics in the periodic system, INS data were analyzed by performing molecular and periodic density functional calculations. Reasonable agreement is achieved, although we note that the poorest agreement is for modes involving hydrogen atoms.  相似文献   

10.
Different types of intramolecular H...H interactions have been analyzed using the MP2/6-311++G(d,p) level of approximation. These are C-H...H-B, C-H...H-Al, C-H...H-C, C-H...H-O, O-H...H-Al and O-H...H-B contacts. Quantum theory of atoms in molecules and natural bond orbitals methods were applied to better understand the nature of these interactions. It was found that some of the species analyzed possess the characteristics of typical hydrogen bonds, such as the O-H...O ones. The electron charge transfer from the Lewis base to the antibonding X-H (for example O-H) orbital of the Lewis acid is one such characteristic. The NBO method may be considered decisive to classify any system as dihydrogen bonded.  相似文献   

11.
Experimental electron densities in coumarin, 1-thiocoumarin, and 3-acetylcoumarin have been analyzed based on the X-ray diffraction data at 90 K. These compounds pack in the crystal lattice with weak C-H...O and C-H...pi interactions, and variations in charge density properties and derived local energy densities have been investigated in the regions of intermolecular interactions. Theoretical charge density calculations on crystals using the B3LYP/6-31G* method show remarkable agreement with the derived properties and energy densities from the experiment. The intermolecular interactions follow an exponential dependence of electron density and energy densities at the bond critical points. The Laplacian follows a "Morse-like" dependence on the length of the interaction line. Based on the set of criteria defined using the theory of "atoms in molecules", it has become possible to distinguish between a hydrogen bond (C-H...O) and a van der Waals interaction (C-H...pi). This has resulted in the identification of a "region of overlap" in terms of electron densities, energy densities, and mutual penetration of the hydrogen and acceptor atoms with respect to the interaction length. This approach suggests a possible tool to distinguish between the two types of interactions.  相似文献   

12.
Interaction of H3O+ or H5O2+ with 1,3-alternate tetrapropoxycalix[4]arene (1) was studied in nitrobenzene and dichloromethane using 1H and 13C NMR including transverse and rotating-frame relaxations and density functional level of theory (DFT) quantum calculations. According to NMR, the ion forms an equimolecular complex with 1 with the equilibrium constant K being 3.97 x 10(3) L.mol(-1) at 296 K. The ions are bound by strong hydrogen bonds to the phenoxy-oxygen atoms of one half of 1 and by a medium-strong hydrogen bond to the pi system of the aromatic rings of the other half. The complex appears to have C(4h) symmetry in NMR even when cooling its solution down to 213 K, which could be due either to a genuine symmetry of the complex (if the ion is H5O2+) or to fast structure averaging by ion exchange processes (if the ion is H3O+). Therefore, the dynamics of the system was studied. Using two independent NMR methods (transverse and rotating-frame relaxation), two different exchange processes were discerned with correlation times 25 x 10(-6) and 5 x 10(-6) s, the first being clearly intermolecular and the other being apparently intramolecular. The energetic aspects of the possible exchange processes were examined by DFT quantum calculations. Rotation of H3O+ ion within one binding site with the energy barrier 8.13 kcal/mol is easily possible. Intermolecular exchange by freeing the ion from the complex has too high a barrier but cooperative interaction of the ion with additional water molecules makes it viable. The intramolecular exchange (or hopping) of the H3O+ ion between the two sites of the molecule is not viable in the classical manner, the barrier being 25.6 kcal/mol. Quantum tunneling of the ion is highly improbable, too. Alternative mechanisms including concerted two-ion intermolecular exchange and cooperative interaction with another bound water molecule including complexation with proton dihydrate H5O2+ are discussed.  相似文献   

13.
The complexes of glyoxal (Gly), methylglyoxal (MGly), and diacetyl (DAc) with water have been studied using Fourier transform infrared (FTIR) matrix isolation spectroscopy and MP2 calculations with 6-311++G(2d,2p) basis set. The analysis of the experimental spectra of the Gly(MGly,DAc)/H2O/Ar matrixes indicates formation of one Gly...H2O complex, three MGly...H2O complexes, and two DAc...H2O ones. All the complexes are stabilized by the O-H...O(C) hydrogen bond between the water molecule and carbonyl oxygen as evidenced by the strong perturbation of the O-H, C=O stretching vibrations. The blue shift of the CH stretching vibration in the Gly...H2O complex and in two MGly...H2O ones suggests that these complexes are additionally stabilized by the improper C-H...O(H2) hydrogen bonding. The theoretical calculations confirm the experimental findings. They evidence the stability of three hydrogen-bonded Gly...H2O and DAc...H2O complexes and six MGly...H2O ones stabilized by the O-H...O(C) hydrogen bond. The calculated vibrational frequencies and geometrical parameters indicate that one DAc..H2O complexes, two Gly...H2O, and three MGly...H2O ones are additionally stabilized by the improper hydrogen bonding between the C-H group and water oxygen. The comparison of the theoretical frequencies with the experimental ones allowed us to attribute the calculated structures to the complexes present in the matrixes.  相似文献   

14.
A variable-low-temperature scanning tunneling microscope (STM) was used to observe oxygen (O2), ethylene (C2H4), and acetylene (C2H2) molecules on a Ag(110) surface and the various complexes that were formed between these two hydrocarbons and oxygen at 13 K. Ethylene molecule(s) were moved to the vicinity of O2 either by STM tunneling electrons at 13 K or thermally at 45 K to form (C2H4)x-O2 (x = 1-4) complexes stabilized by C-H...O hydrogen bonding. Acetylene-oxygen complexes involving one or two acetylene molecules were observed.  相似文献   

15.
Microsolvated formamide clusters have been generated in a supersonic jet expansion and characterized using Fourier transform microwave spectroscopy. Three conformers of the monohydrated cluster and one of the dihydrated complex have been observed. Seven monosubstituted isotopic species have been measured for the most stable conformer of formamide...H(2)O, which adopts a closed planar ring structure stabilized by two intermolecular hydrogen bonds (N-H...O(H)-H...O=C). The two higher energy forms of formamide...H(2)O have been observed for the first time. The second most stable conformer is stabilized by a O-H...O=C and a weak C-H...O hydrogen bond, while, in the less stable form, water accepts a hydrogen bond from the anti hydrogen of the amino group. For formamide...(H(2)O)(2), the parent and nine monosubstituted isotopic species have been observed. In this cluster the two water molecules close a cycle with the amide group through three intermolecular hydrogen bonds (N-H...O(H)-H...O(H)-H...O=C), the nonbonded hydrogen atoms of water adopting an up-down configuration. Substitution (r(s)) and effective (r(0)) structures have been determined for formamide, the most stable form of formamide...H(2)O and formamide...(H(2)O)(2). The results on monohydrated formamide clusters can help to explain the observed preferences of bound water in proteins. Clear evidence of sigma-bond cooperativity effects emerges when comparing the structures of the mono- and dihydrated formamide clusters. No detectable structural changes due to pi-bond cooperativity are observed on formamide upon hydration.  相似文献   

16.
The characteristics of the interaction between the pi cloud of naphthalene and up to two H2O or H2S molecules were studied. Calculations show that clusters formed by naphthalene and one H2O or H2S molecule have similar geometric features, and also present similar interaction energies. Our best estimates for the interaction energy amount to -2.95 and -2.92 kcal/mol for H2O and H2S, respectively, as obtained with the CCSD(T) method. Calculations at the MP2 level employing large basis sets should be avoided because they produce highly overestimated interaction energies, especially for hydrogen sulfide complexes. The MPWB1K functional, however, provides values pretty similar to those obtained with the CCSD(T) method. Although the magnitude of the interaction is similar with both H2X molecules, its nature is somewhat different: the H2O complex presents electrostatic and dispersion contributions of similar magnitude, whereas for H2S the interaction is dominated by dispersion. In clusters containing two H2X molecules several minima were characterized. In water clusters, the total interaction energy is dominated by the presence of a O-H...O hydrogen bond and, as a consequence, structures where this contact is present are the most stable. However, clusters containing H2S show structures with no interaction between H2S moieties which are as stable as the hydrogen bonded ones, because they allow an optimal H2S...naphthalene interaction, which is stronger than the S-H...S contact. Therefore it is possible that in larger polycycles hydrogen sulfide molecules will be spread onto the surface maximizing S-H...pi interactions rather than aggregated, forming H2S clusters.  相似文献   

17.
The title compounds, C16H16O5 (I) and C16H16O5·H2O (II), were structurally characterized by single-crystal X-ray diffraction. Compound I crystallizes in monoclinic space group P21/c with a = 10.5574(10), b = 8.3576(9), c = 16.5528(16) , β = 91.762(3)°, Z = 4, R = 0.0524 and wR = 0.1084. The molecules are jointed into a chain by intermolecular O-H···O and C-H···O hydrogen bonds, which form layers parallel to (001). The chains run along the [110] and [110] directions alternatively layer by layer, and are assembled into a network by intermolecular O-H···O (carboxyl) hydrogen bonds. On the other hand, the hydrate complex (II) crystallizes in the triclinic space group P1 with a = 5.1451(2), b = 10.4583(4), c = 14.8267(5) , α = 70.900(2), β = 82.478(2), γ = 81.359(2)°, Z = 2, R = 0.0393 and wR = 0.0983. The molecules are linked into infinite two-dimensional ribbons by O-H···O (carbonyl) and solvent-bridged O-H···O hydrogen bonds.  相似文献   

18.
In this work, we report the structural studies on the solid state of two benzodiazacoronads that form chiral and achiral crystals. Crystals have to be considered as a two-component system consisting of an organic unit and a water molecule in 1:1 ratio. Both components play an important role in the crystal structure. The strong (O-H...O, N-H...O) and weak (C-H...O) intermolecular hydrogen bonds are responsible for phase organization and, in consequence, formation of chiral or achiral crystals. The alignment of the water molecule with respect to the macrocycle is different for samples 1 and 2. Removal of water from the crystal lattice of 1 is reversible. Formation of chiral cocrystals from two different achiral molecules by self-assembly is well-known. However, in this paper, we show that the water molecule can be an important achiral cofactor responsible for chiral crystallization.  相似文献   

19.
An in-depth analysis of a set of 21 layered structures of metallic pseudopolymorphs of general formulation, beta'-(BEDT-TTF)(4) x (guest)(n) x [Re(6)Q(6)Cl(8)], (BEDT-TTF=bis-ethylenedithiotetrathiafulvalene; Q = S, Se; guest = H(2)O, 1,4-dioxane, THF, CCl(4), C(2)H(5)OH, CHCl(3), CH(2)ClI, CH(2)ClBr, CH(2)Cl(2), CH(2)OH-CH(2)OH, C(5)H(5)N, CH(3)COCH(3), 2-hydroxy-tetrahydrofuran, CH(3)CN, CS(2), C(6)H(6)), with diverse low-temperature behaviors, which differ solely by the nature of the cosolvent molecule selectively included during the electrocrystallization process, reveals a precise set of weak HO-H...Cl-mu-Re, (C-H)(BEDT-TTF)...Cl-mu-Re, C-H...O(guest), (C-H)(guest)...Cl-mu-Re hydrogen bonds at the organic-inorganic interface, none of which dominates any of the others and whose balance is adjusted upon substitution of one guest molecule by another. The electronic structure of the host adjusts to the weak perturbation imposed by exchanging the guest molecules and by balancing the former interfacial interactions; this correlates to a net activation of up to 0.1 eV of the energy of the HOMO level of one of the two donors, while keeping the pattern of HOMO-HOMO intermolecular interactions in the donor layer essentially unaltered. It is suggested that this controls the stability of the metallic state at low temperature or the occurrence of a metal-to-insulator phase transition for particular guests along the series. It is concluded that by allowing for numerous tiny modifications at the organic-inorganic interface within a single, robust host structure, one sees a concerted, inherently weak structural response of the system that is proportional to the magnitude of the underlying, equally weak activation of the HOMO energy of a fraction of the pi-donor molecules within the slabs; this has a sizeable influence on the macroscopic transport properties of the system.  相似文献   

20.
Although being composed of trivalent ions, the crystal structure of the supramolecular intercluster compound [Au9(PPh3)8]2[V10O28H3]2 is dominated by short-range intermolecular interactions, i.e., hydrogen bonds, and C-H/pi interactions, avoiding a simple AB-type packing.  相似文献   

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