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1.
Chemical double-mutant cycles have been used to quantify intermolecular functional-group interactions in H-bonded zipper complexes in chloroform. If the same interaction is measured in zippers of different overall stability, the double-mutant cycles can be combined to produce a triple-mutant box. This construct quantifies cooperativity between the functional group interaction of interest and the other interactions that are used to change the overall stability of the complexes. The sum of two edge-to-face aromatic interactions (-2.9 +/- 0.5 kJ mol-1) is shown to be insensitive to changes of up to 13.7 +/- 0.2 kJ mol-1 in the overall stability of the complex. In principle, enthalpic cooperative effects caused by entropy-enthalpy compensation could perturb the measurement of intermolecular interactions when using the double-mutant cycle approach, but these experiments show that, for this system, the magnitude of the effect lies within the error of the measurements.  相似文献   

2.
MP2 calculations with cc-pVTZ basis set were used to analyze intermolecular interactions in F(3)CX···HMgH···Y and F(3)CX···Y···HMgH triads (X = Cl, Br; Y = HCN, and HNC) which are connecting with three kinds of unusual weak interactions, namely halogen-hydride, dihydrogen, and σ-hole. To understand the properties of the systems better, the corresponding dyads are also studied. Molecular geometries, binding energies, and infrared spectra of monomers, dyads, and triads were investigated at the MP2/cc-pVTZ computational level. Particular attention is given to parameters such as cooperative energies, cooperative dipole moments, and many-body interaction energies. Those complexes with simultaneous presence of a σ-hole bond and a dihydrogen bond show cooperativity energy ranging between -1.02 and -2.31 kJ mol(-1), whereas those with a halogen-hydride bond and a dihydrogen bond are diminutive, with this energetic effect between 0.1 and 0.63 kJ mol(-1). The electronic properties of the complexes have been analyzed using the molecular electrostatic potential (MEP), the electron density shift maps, and the parameters derived from the atoms in molecules (AIM) methodology.  相似文献   

3.
A model beta-hairpin peptide has been used to investigate the context-dependent contribution of cross-strand Lys-Glu interactions to hairpin stability. We have mutated two Ser-Lys interstrand pairs to Glu-Lys salt bridges, one close to the type I' Asn-Gly turn sequence (Ser6 --> Glu), and one close to the N- and C-termini (Ser15 --> Glu). Each individual interaction contributes approximately 1.2-1.3 kJ mol(-1) to stability; however, introducing the two salt bridges simultaneously produces a much larger overall contribution (-3.6 kJ mol(-1)) consistent with an important role for preorganization and cooperativity in determining the energetics of weak interactions. We compare and contrast CD and NMR data on the highly folded hairpin with the two Glu-Lys pairs to shed light on the nature of the folded state in water. We show that large cosolvent-induced changes in the CD spectrum, in contrast with the modest effects observed on Halpha chemical shifts, support a hydrophobically collapsed entropy-driven conformation in water whose stability is modulated by long-range Coulombic interactions from the Glu-Lys interactions. Cosolvent stabilizes the structure enthalpically, as is evident from CD melting profiles.  相似文献   

4.
Possible mechanisms for intermolecular exchange between coordinated and solvent water in the complexes Y(TTA)(3)(OH(2))(2) and Y(TTA)(3)(TBP)(OH(2)) and intermolecular exchange between free and coordinated HTTA in Y(TTA)(3)(OH(2))(HTTA) and Y(TTA)(3)(TBP)(HTTA) have been investigated using ab initio quantum chemical methods. The calculations comprise both structures and energies of isomers, intermediates and transition states. Based on these data and experimental NMR data (Part 2) we have suggested intimate reaction mechanisms for water exchange, intramolecular exchange between structure isomers and intermolecular exchange between free HTTA and coordinated TTA. A large number of isomers are possible for the complexes investigated, but only some of them have been investigated, in all of them the most stable geometry is a more or less distorted square anti-prism or bicapped trigonal prism; the energy differences between the various isomers are in general small, less than 10 kJ mol(-1). 9-coordinated intermediates play an important role in all reactions. Y(TTA)(3)(OH(2))(3) has three non-equivalent water ligands that can participate in ligand exchange reactions. The fastest of these exchanging sites has a QM activation energy of 18.1 kJ mol(-1), in good agreement with the experimental activation enthalpy of 19.6 kJ mol(-1). The mechanism for the intramolecular exchange between structure isomers in Y(TTA)(3)(OH(2))(2) involves the opening of a TTA-ring as the rate determining step as suggested by the good agreement between the QM activation energy and the experimental activation enthalpy 47.8 and 58.3 J mol(-1), respectively. The mechanism for the intermolecular exchange between free and coordinated HTTA in Y(TTA)(3)(HTTA) and Y(TTA)(3)(TBP)(HTTA) involves the opening of the intramolecular hydrogen bond in coordinated HTTA followed by proton transfer to coordinated TTA. This mechanism is supported by the good agreement between experimental activation enthalpies (within parenthesis) and calculated activation energies 68.7 (71.8) and 35.3 (38.8) kJ mol(-1). The main reason for the difference between the two systems is the much lower energy required to open the intramolecular hydrogen bond in the latter. The accuracy of the QM methods and chemical models used is discussed.  相似文献   

5.
6.
Halogen-hydride interactions between Z-X (Z = CN, NC and X = F, Cl, Br) as halogen donor and H-Mg-Y (Y = H, F, Cl, Br, CH(3)) as electron donor have been investigated through the use of Becke three-parameter hybrid exchange with Lee-Yang-Parr correlation (B3LYP), second-order M?ller-Plesset perturbation theory (MP2), and coupled-cluster single and double excitation (with triple excitations) [CCSD(T)] approaches. Geometry changes during the halogen-hydride interaction are accompanied by a mutual polarization of both partners with some charge transfer occurring from the electron donor subunit. Interaction energies computed at MP2 level vary from -1.23 to -2.99 kJ/mol for Z-F···H-Mg-Y complexes, indicating that the fluorine interactions are relatively very weak but not negligible. Instead, for chlorine- and bromine-containing complexes the interaction energies span from -5.78 to a maximum of -26.42 kJ/mol, which intimate that the interactions are comparable to conventional hydrogen bonding. Moreover, the calculated interaction energy was found to increase in magnitude with increasing positive electrostatic potential on the extension of Z-X bond. Analysis of geometric, vibrational frequency shift and the interaction energies indicates that, depending on the halogen, CN-X···H interactions are about 1.3-2.0 times stronger than NC-X···H interactions in which the halogen bonds to carbon. We also identified a clear dependence of the halogen-hydride bond strength on the electron-donating or -withdrawing effect of the substituent in the H-Mg-Y subunits. Furthermore, the electronic and structural properties of the resulting complexes have been unveiled by means of the atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Finally, several correlative relationships between interaction energies and various properties such as binding distance, frequency shift, molecular electrostatic potential, and intermolecular density at bond critical point have been checked for all studied systems.  相似文献   

7.
硝仿肼离子对相互作用的密度泛函理论研究   总被引:1,自引:0,他引:1  
用密度泛函理论(DFT)方法,在B3LYP/6-31+G**水平下,求得硝仿肼离子对体系势能面上2种全优化构型.经基组叠加误差(BSSE)和零点能校正,求得离子对最大相互作用能为-420.03kJ/mol,肼和硝仿离子化所需能量可由该值得到完全补偿.离子对间键的主要贡献为库仑作用,但键鞍点上的电子密度值表明共价作用也有显著的贡献.基于统计热力学求得相关体系的热力学性质,298.2K时由自由离子形成最稳定离子对的最大焓变和最大自由能变化分别为-419.72和-376.61kJ/mol  相似文献   

8.
Accurate estimation of individual intramolecular hydrogen bond (H-bond) energies is an intricate task for multiply H-bonded systems. In such cases, the hydrogen bond strengths could be highly influenced by the cooperative interactions, for example, those between hydroxyl groups in sugars. In this work, we use the recently proposed molecular tailoring approach-based quantification (Deshmukh, Gadre, and Bartolotti, J Phys Chem A 2006, 110, 12519) to the extended systems of cyclodextrins (CDs). Further, the structure and stability of different conformers of α-, β-, and γ-CDs are explained based on the energetics and cooperative contribution to the strength of these H-bonds. The estimated O-H···O H-bond energies in the various CD conformers are found to vary widely from 1.1 to 8.3 kcal mol(-1). The calculated energy contributions to cooperativity toward the H-bond strengths fall in the range of 0.25-2.75 kcal mol(-1).  相似文献   

9.
Cooperativity is a hallmark of spontaneous biopolymer folding. The presence of intermolecular interactions could create off-pathway misfolding structures and suppress folding cooperativity. This raises the hypothesis that thermodynamic competitivity between off-pathway misfolding and on-pathway folding may intervene with cooperativity and govern biopolymer folding dynamics under conditions permitting large-scale intermolecular interactions. Here we report direct imaging and theoretical modeling of thermodynamic competitivity between biopolymer folding and misfolding under such conditions, using a two-dimensional array of proton-fueled DNA molecular motors packed at the maximal density as a model system. Time-resolved liquid-phase atomic force microscopy with enhanced phase contrast revealed that the misfolding and folding intermediates transiently self-organize into spatiotemporal patterns on the nanoscale in thermodynamic states far away from equilibrium as a result of thermodynamic competitivity. Computer simulations using a novel cellular-automaton network model provide quantitative insights into how large-scale intermolecular interactions correlate the structural dynamics of individual biomolecules together at the systems level.  相似文献   

10.
The complex dications in the cooperative spin-crossover compound [FeL(2)][BF(4)](2) (2,6-di(pyrazol-1-yl)pyridine) pack through pi-pi interactions into a 2-D layered structure (a "terpyridine embrace" motif). The effects of doping the larger ClO(4)(-) ion into this lattice have been investigated. The bulk solids [FeL(2)][ClO(4)](x)[BF(4)](2-x) are isostructural with [FeL(2)][BF(4)](2) when x = 0.30 and 0.98, and isostructural with (structurally distinct) [FeL(2)][ClO(4)](2) when x = 1.89. When x = 1.68, powder samples are a mixture of both phases, but crystalline material adopts purely the ClO(4)(-) structure. Increasing the perchlorate content in the lattice for 0 < or =x< or = 1.68 causes a small decrease in T(1/2) and a narrowing of hysteresis in their spin-crossover, but with no significant reduction in cooperativity. It also leads to more pronounced decreases in DeltaH [by up to 3.2(5) kJ mol(-1)] and DeltaS [by up to 10(2) J mol(-1) K(-1)] for the transition by DSC. Single crystals of formula [FeL(2)][ClO(4)](y)[BF(4)](2-y) (y = 0.44 and 1.13) are isostructural with the pure BF(4)(-) salt. While their molecular structures are indistinguishable, the distances between cations in the lattice increase in the doped materials. Weakening of intermolecular pi-pi interactions between cations is the likely reason for the reduced enthalpy of spin-crossover as x increases. However, the biggest stuctural change is an increase in the spacing between the 2-D layers with increased ClO(4)(-). These results suggest that cooperativity in this material is transmitted within the terpyridine embrace layers.  相似文献   

11.
We examine the adsorption of CH(4) on the MgO(001) surface by a hybrid approach. It combines MP2 calculations with extrapolation to the complete basis set limit for the adsorption site and the CH(4)-CH(4) pair interactions in the adsorbate layer, with DFT+dispersion calculations under periodic boundary conditions for the whole system. To the total binding energy of 10.7 kJ mol(-1), the DFT+D(ispersion) correction contributes 0.7 kJ mol(-1) only, showing that the Mg(9)O(9) two-layer surface model is an excellent choice and that the interaction between the CH(4) molecules in the adsorbate layer is dominated by pair interactions. Contributions due to relaxation of the atom positions of 0.6 kJ mol(-1) (evaluated at DFT+dispersion) and of higher order correlation effects of 2.0 kJ mol(-1) (evaluated by CCSD(T)) yield a final estimate of 13.3 kJ mol(-1). To this total adsorption energy, the lateral interactions between the CH(4) molecules in the adsorbate layer contribute substantially, 4.1 kJ mol(-1)."Observed" desorption energies of 15.3 and 16.0 kJ mol(-1) have been derived from the observed Arrhenius desorption barriers (12.6 and 13.1 kJ mol(-1)) using thermal enthalpy contributions and a substantial zero-point energy (4.2 kJ mol(-1)) calculated from DFT+D vibrational frequencies. The comparison shows that our final hybrid MP2?:?PBE+D+ΔCCSD(T) estimate has reached chemical accuracy. It misses 2-3 kJ mol(-1) of binding only, which is most likely due to missing higher order correlation effects.PBE+D(ispersion) itself yields an adsorption energy that agrees within 1 kJ mol(-1) with our final hybrid MP2?:?PBE+D+ΔCCSD(T) estimate.  相似文献   

12.
We report here solution NMR relaxation measurements that show millisecond time-scale intersubunit dynamics in the homopentameric B subunit (VTB) of the toxin derived from Escherichia coli O157. These data are consistent with interconversion between an axially symmetric form and a low-abundance ( approximately 10%, 45 degrees C) higher energy form. The higher energy state is depopulated on binding of a novel bivalent analogue (P(k) dimer) of the natural carbohydrate acceptor globotriaosylceramide. The isothermal titration calorimetry isotherm for the binding of P(k) dimer to VTB is consistent with a five-site sequential binding model which assumes that cooperative effects arise through communication only between neighboring binding sites. The resulting thermodynamic parameters (K(a1) = 114 +/- 2.2 M(-1), K(a2) = 283 +/- 4.5 M(-1), DeltaH(1) degrees = -116.3 +/- 0.55 kJ/mol, and DeltaH(2) degrees = -50.3 +/- 0.11 kJ/mol) indicate favorable entropic cooperativity that has not previously been observed in multivalent systems.  相似文献   

13.
We present theoretically as well as experimentally determined thermochemical data of the non-covalent interactions in different axle-substituted pseudorotaxanes. The overall interaction energy lies in the region of 35 kJ mol(-1), independent of the substitution pattern at the axle. Because rearrangement energies of 7 and 3 kJ mol(-1) are required for wheel and axle, respectively, the sum of the net interactions of individual non-covalent bonds must exceed 10 kJ mol(-1) to achieve a successful host-guest interaction. The geometrical analysis shows three hydrogen bonds, and the close inspection of the individual dipole moments as well as the individual hydrogen bonds reveals trends according to the different functional groups at the axle. The individual trends for the different hydrogen bonds almost lead to a cancellation of the substitution effects. From solvent-effect considerations it can be predicted that the pseudorotaxane is stable in CHCl(3) and CH(2)Cl(2), whereas it would dethread in water. Comparing experimentally and theoretically calculated Gibbs free enthalpies, we find reasonable agreement if an exchange reaction of one solvent molecule instead of the direct formation reaction is considered.  相似文献   

14.
Complexes between ammonia, water, or hydrogen fluoride and adenine, guanine, or their 8-oxo derivatives are investigated using density-functional theory. The binding strengths of the neutral and (N9) anionic complexes are considered for a variety of purine binding sites. The effects of hydrogen-bonding interactions on the (N9) acidity of the purine derivatives are considered as a function of the molecule bound and the binding site. It is found that hydrogen-bonding interactions with one molecule can increase the acidity of purine derivatives by up to 60 kJ mol(-1). The (calculated) simultaneous effects of up to four molecules on the acidity of the purine derivatives are also considered. Our data suggest that the effects of more than one molecule on the acidity of the purines are generally less than the sum of the individual (additive) effects, where the magnitude of the deviation from additivity increases with the number, as well as the acidity, of molecules bound. Nevertheless, the increase in the acidity due to additional hydrogen-bonding interactions is significant, where the effect of two, three, or four hydrogen-bonding interactions can be as large as approximately 95, 115, and 130 kJ mol(-1), respectively. The present study provides a greater fundamental understanding of hydrogen-bonding interactions involving the natural purines, as well as those generated through oxidative DNA damage, which may aid the understanding of important biological processes.  相似文献   

15.
The properties of six dihydrogen-bonded (DHB) dimers with the BeH2 molecule as a proton acceptor were calculated by MP2, CCSD(T) and B3LYP methods. The structural, energetic and spectroscopic parameters are presented and analyzed in terms of their possible correlation with the interaction energy and the intermolecular H...H separation. The symmetry-adapted perturbation theory (SAPT) calculations were performed to gain more insight into the nature of the H...H interactions. The studied complexes are divided into three groups based on the calculated intermolecular distances and the interaction energies which range from approximately -1 to -42 kJ mol(-1). The analysis of the interaction energy components indicates that, in contrast to conventional hydrogen bonds, the induction energy is the most important term in the BeH2NH4+ complex. On the other hand, there is no sharp boundary between the DHB complexes classified as hydrogen bonded and van der Waals systems. The complexation-induced changes in vibrational frequencies and in proton shielding constants show a relationship with the interaction energy. The values of the 2hJXH and 3hJBeX coupling constants correlate well with the interaction energy and with the intermolecular distance.  相似文献   

16.
By using 13C MAS NMR spectroscopy (MAS = magic angle spinning), the conversion of selectively 13C-labeled n-butane on zeolite H-ZSM-5 at 430-470 K has been demonstrated to proceed through two pathways: 1) scrambling of the selective 13C-label in the n-butane molecule, and 2) oligomerization-cracking and conjunct polymerization. The latter processes (2) produce isobutane and propane simultaneously with alkyl-substituted cyclopentenyl cations and condensed aromatic compounds. In situ 13C MAS NMR and complementary ex situ GC-MS data provided evidence for a monomolecular mechanism of the 13C-label scrambling, whereas both isobutane and propane are formed through intermolecular pathways. According to 13C MAS NMR kinetic measurements, both pathways proceed with nearly the same activation energies (E(a) = 75 kJ mol(-1) for the scrambling and 71 kJ mol(-1) for isobutane and propane formation). This can be rationalized by considering the intermolecular hydride transfer between a primarily initiated carbenium ion and n-butane as being the rate-determining stage of the n-butane conversion on zeolite H-ZSM-5.  相似文献   

17.
The paper reports the synthesis and detailed characterization of two new Fe(II) compounds: [Fe(pyim)(2)(bpen)](ClO(4))(2).2C(2)H(5)OH (2) and [Fe(pyim)(2)(bpe)](ClO(4))(2).C(2)H(5)OH (3) (pyim = 2-(2-pyridyl)imidazole, bpen = 1,2-bis(4-pyridyl)ethane, and bpe = 1,2-bis(4-pyridyl)ethene). Both compounds and the earlier synthesized [Fe(pyim)(2)(bpy)](ClO(4))(2).2C(2)H(5)OH (1) (bpy = 4,4'-bipyridine) form a family of one-dimensional spin crossover coordination polymers. Variable-temperature magnetic susceptibility measurements and M?ssbauer spectroscopy have revealed rather gradual spin transitions centered at 176 and 198 K for 2 and 3, respectively. The fitting of magnetic properties with the regular solution model leads to the enthalpy and entropy of spin transitions and the cooperativity parameter equal to DeltaH = 12.3 kJ mol(-1), DeltaS = 68.5 J mol(-1) K(-1), Gamma = 1.80 kJ mol(-1) for 2 and DeltaH = 13.6 kJ mol(-1), DeltaS = 68.1 J mol(-1) K(-1), Gamma = 2.05 kJ mol(-1) for 3. The crystal structures of 2 and 3, resolved by X-ray diffraction at 293 K, belong to the monoclinic space group C2/c (Z = 4). Both compounds display a one-dimensional infinite zigzag-chain structure. The polymer chains are stacked into two-dimensional sheets through intermolecular pi-interactions. The crystal packing of both compounds encloses two kinds of channels in which the counter ions and ethanol molecules are inserted. The DFT calculations of binuclear fragments extracted from three polymers resulted in the energy gaps between the LS and HS states being ordered as the observed transition temperatures. The influence of bridging ligands in the studied family of compounds was found in the modulation of the energy gap between the LS and HS states, leading to different transition temperatures.  相似文献   

18.
The chemical double mutant cycle approach has been used to investigate substituent effects on intermolecular interactions between aromatic rings and pentafluorophenyl pi-systems. The complexes have been characterised using 1H and 19F NMR titrations, X-ray crystal structures of model compounds and molecular mechanics calculations. In the molecular zipper system used for these experiments, H-bonds and the geometries of the interacting surfaces favour the approach of the edge of the aromatic ring with the face of the pentafluorophenyl pi-system. The interactions are generally repulsive and this repulsion increases with more electron-withdrawing substituents up to a limit of +2.2 kJ mol(-1), when the complex distorts to minimise the unfavourable interaction. Strongly electron-donating groups cause a change in the geometry of the aromatic interaction and attractive stacking interactions are found (-1.6 kJ mol(-1) for NMe2). These results are generally consistent with an electrostatic model: the polarisation of the pentafluorophenyl ring leads to a partial positive charge located at the centre and this leads to repulsive interactions with the positive charges on the protons on the edge of the aromatic ring; when the aromatic ring has a high pi-electron density there is a large electrostatic driving force in favour of the stacked geometry which places this pi-electron density over the centre of the positive charge on the pentafluorophenyl group.  相似文献   

19.
Ab initio and DFT calculations reveal that acyl radicals add to imines and electron-rich olefins through simultaneous SOMO --> pi*, pi --> SOMO, and HOMO --> pi*C=O interactions between the radical and the radicalophile. At the CCSD(T)/aug-cc-pVDZ//QCISD/cc-pVDZ level, energy barriers of 15.6 and 17.9 kJ mol(-1) are calculated for the attack of the acetyl radical at the carbon and nitrogen ends of methanimine, respectively. These barriers are 17.1 and 20.4 kJ mol(-1) at BHandHLYP/cc-pVDZ. In comparison, barriers of 34.0 and 23.4 kJ mol(-1) are calculated at BHandHLYP/cc-pVDZ for reaction of the acetyl radical at the 1- and 2-positions in aminoethylene, repectively. Natural bond orbital (NBO) analysis at the BHandHLYP/6-311G** level of theory reveals that SOMO --> pi*imine, pi imine--> SOMO, and LPN --> pi*C=O interactions are worth 90, 278, and 138 kJ mol-1, respectively, in the transition state (2) for reaction of acetyl radical at the nitrogen end of methanimine; similar interactions are observed for the chemistry involving aminoethylene. These multiorbital interactions are responsible for the unusual motion vectors associated with the transition states involved in these reactions. NBO analyses for the remaining systems in this study support the hypothesis that the acetyl radical is ambiphilic in nature.  相似文献   

20.
Using FTIR and Raman spectroscopy, the formation of halogen bonded complexes of the trifluorohalomethanes CF(3)Cl, CF(3)Br and CF(3)I with dimethyl sulfide (DMS) dissolved in liquid krypton has been investigated. For CF(3)Br and CF(3)I, evidence was found for the formation of C-XS halogen bonded 1:1 complexes. At higher concentrations of CF(3)I weak absorptions due to a 2:1 complex were also observed. Using spectra recorded at temperatures between 118 and 163 K, the complexation enthalpies for the complexes were determined to be -9.5(5) kJ mol(-1) for CF(3)Br·DMS, -17.4(1) kJ mol(-1) for CF(3)I·DMS and -30.8(16) kJ mol(-1) for (CF(3)I·)(2)DMS. The results from the cryospectroscopic study are compared with ab initio calculations at the MP2/aug-cc-pVDZ(-PP) level. Apart from vibrational modes localized in the trifluorohalomethanes and the DMS moieties, for both CF(3)Br and CF(3)I, an additional band, which we assign as the intermolecular stretching mode in the complex, was identified in the infrared and Raman spectra.  相似文献   

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