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1.
The spectral and structural changes, caused by the conversion of the 3-hydroxybenzaldehyde molecule into the corresponding oxyanion have been studied by IR spectra, and MP2 and DFT force field calculations. The conversion causes a 13 cm(-1) decrease in the frequency of the carbonyl stretching band nu(Cz=O), a 1.3-fold increase in its integrated intensity, strong intensity increases (2.1-5.3-fold) of the aromatic skeletal nu8 and nu19 as well as formyl nu(CH) bands. According to the calculations the oxyanionic charge is delocalized over aldehyde group (0.37 e-), phenylene ring (0.12 e-) and oxyanionic center (0.52 e-). The conversion into the oxyanion leads to geometry changes in the whole species, but it remains planar.  相似文献   

2.
The spectral and structural changes, caused by the conversion of the vanillin molecule into the corresponding oxyanion have been studied by IR spectra and normal coordinate calculations within the Onsager self-consistent reaction field (SCRF) model, using a density functional theory (DFT) method at the Becke3LYP/6-31+G** level. Structures of all conformational isomers of vanillin and of its anion have been located, as well as their total and relative energies have been determined. The conversion leads to geometry changes in the whole species, due to the strong O-/acceptor polar resonance through the para phenylene ring. The conversion causes a 41 cm(-1) decrease in the frequency of the carbonyl stretching band nu(C=O), strong intensity increases (1.6 - 7.2-fold) of the aromatic skeletal nu8 and nu19 as well as formyl nu(CH) bands. According to the calculations the oxyanionic charge is delocalized over aldehyde group (0.25 e-), phenylene ring (0.13 e-), methoxy group (0.07 e-) and oxyanyonic center (0.55 e-).  相似文献   

3.
The spectral and structural changes, caused by the conversion of phenylpropanedinitrile (phenylmalononitrile) into the carbanion, have been followed by IR spectra, ab initio HF, MP2 and DFT BLYP force field calculations. In agreement between theory and experiment, the conversion is accompanied with strong frequency decreases (with 114 cm(-1), mean value) of the cyano stretching bands nu(C triple bond N), dramatic increases in the corresponding integrated intensities (136-fold, total value), strong enhancement of the nu(C triple bond N) vibrational coupling and other essential spectral changes. According to the calculations, the strongest structural changes take place at the carbanionic center: (i) shortenings of the Cz-Ph and Cz-CN bonds with 0.064-0.092 A, and increases in the corresponding bond orders with 0.14-0.21 U; (ii) simultaneous enlargements of the bond angles at the same carbon atom with 7.6 degrees -9.7 degrees, as from tetrahedral its configuration becomes trigonal. The carbanionic charge is distributed between the two cyano groups (0.44-0.52 e(-)), phenyl ring (0.31-0.34 e(-)) and carbanionic center (0.14-0.25 e(-)). The formation of moderately strong (CH(3))(2)S=O...H-C(CN)(2)C(6)H(5) hydrogen bonds has been found experimentally.  相似文献   

4.
The structure of o-vanillin molecule and its oxyanion have been studied by density functional theory (DFT), employing the B3LYP functional and 6-311++G** basis set. All conformational isomers of o-vanillin and of its anion have been located and their relative energies have been determined. The IR spectral changes, caused by the conversion of the molecule into the corresponding oxyanion have been studied. In a general agreement between theory and experiment, the conversion causes a frequency decrease of the carbonyl stretching band ν(CO) and essential intensity increases of the aromatic skeletal bands as well as methyl stretching band ν(CH3). According to the NBO electric charge analysis, the oxyanionic center bears 60% of the whole anionic net charge.  相似文献   

5.
Prior site-directed mutagenesis studies in bacterial ketosteroid isomerase (KSI) reported that substitution of both oxyanion hole hydrogen bond donors gives a 10(5)- to 10(8)-fold rate reduction, suggesting that the oxyanion hole may provide the major contribution to KSI catalysis. But these seemingly conservative mutations replaced the oxyanion hole hydrogen bond donors with hydrophobic side chains that could lead to suboptimal solvation of the incipient oxyanion in the mutants, thereby potentially exaggerating the apparent energetic benefit of the hydrogen bonds relative to water-mediated hydrogen bonds in solution. We determined the functional and structural consequences of substituting the oxyanion hole hydrogen bond donors and several residues surrounding the oxyanion hole with smaller residues in an attempt to create a local site that would provide interactions more analogous to those in aqueous solution. These more drastic mutations created an active-site cavity estimated to be ~650 ?(3) and sufficient for occupancy by 15-17 water molecules and led to a rate decrease of only ~10(3)-fold for KSI from two different species, a much smaller effect than that observed from more traditional conservative mutations. The results underscore the strong context dependence of hydrogen bond energetics and suggest that the oxyanion hole provides an important, but moderate, catalytic contribution relative to the interactions in the corresponding solution reaction.  相似文献   

6.
The microwave spectra of (methylenecyclopropyl)methanol (H(2)C=C(3)H(3)CH(2)OH) and one deuterated species (H(2)C=C(3)H(3)CH(2)OD) have been investigated in the 20-80 GHz spectral range. Accurate spectral measurements have been performed in the 40-80 GHz spectral interval. The spectra of two rotameric forms, denoted conformer I and conformer IX, have been assigned. Both these rotamers are stabilized by intramolecular hydrogen bonds formed between the hydrogen atom of the hydroxyl group and the pseudo-pi electrons on the outside of the cyclopropyl ring, the so-called "banana bonds". The carbon-carbon bond lengths in the ring are rather different. The bonds adjacent to the methylene group (H(2)C=) are approximately 7 pm shorter that the carbon-carbon bond opposite to this group. It is found from relative intensity measurements of microwave transitions that conformer IX, in which the hydrogen bond is formed with the banana bonds of the long carbon-carbon bond, is 0.4(3) kJ/mol more stable than conformer I, where the hydrogen bond is formed with the pseudo-pi electrons belonging to the shortest carbon-carbon bond of the ring. The microwave study has been augmented by quantum chemical calculations at the MP2/6-311++G, G3 and B3LYP/6-311++G levels of theory.  相似文献   

7.
The generalized gradient approximation based on density functional theory is used to analyze the geometric and electronic properties of Si @ C(74). It is found that among the five possible optimized geometries of Si @ C(74), the most favorable endohedral site of Si atom is under the center of a pentagon ring on the sigma(h) plane, i.e., Si @ C(74)-5, which is different from the center stable site for Si in C(74) calculated by the semiempirical molecular orbital calculations and molecular mechanics calculations, and it is also different from the stable site, i.e., under a [6, 6] bond along the C(2) axis on the sigma(h) plane in C(74) for metal atoms Ba, Ca, and Eu. The deformation charge density on the sigma(h) plane reveals that the Si-C bonds in Si @ C(74)-5 have covalent character, while the Mulliken charge analysis together with a longer Si-C bond length reveals that the Si-C bonds in Si @ C(74)-5 have ionic character. Therefore, we infer that Si-C bonds in Si @ C(74)-5 contain both covalent and ionic characters.  相似文献   

8.
The potential-energy surface of the first excited state of the 11-cis-retinal protonated Schiff base (PSB11) chromophore has been studied at the density functional theory (DFT) level using the time-dependent perturbation theory approach (TDDFT) in combination with Becke's three-parameter hybrid functional (B3LYP). The potential-energy curves for torsion motions around single and double bonds of the first excited state have also been studied at the coupled-cluster approximate singles and doubles (CC2) level. The corresponding potential-energy curves for the ground state have been calculated at the B3LYP DFT and second-order M?ller-Plesset (MP2) levels. The TDDFT study suggests that the electronic excitation initiates a turn of the beta-ionone ring around the C6-C7 bond. The torsion is propagating along the retinyl chain toward the cis to trans isomerization center at the C11=C12 double bond. The torsion twist of the C10-C11 single bond leads to a significant reduction in the deexcitation energy indicating that a conical intersection is being reached by an almost barrierless rotation around the C10-C11 single bond. The energy released when passing the conical intersection can assist the subsequent cis to trans isomerization of the C11=C12 double bond. The CC2 calculations also show that the torsion barrier for the twist of the retinyl C10-C11 single bond adjacent to the isomerization center almost vanishes for the excited state. Because of the reduced torsion barriers of the single bonds, the retinyl chain can easily deform in the excited state. Thus, the CC2 and TDDFT calculations suggest similar reaction pathways on the potential-energy surface of the excited state leading toward the conical intersection and resulting in a cis to trans isomerization of the retinal chromophore. According to the CC2 calculations the cis to trans isomerization mechanism does not involve any significant torsion motion of the beta-ionone ring.  相似文献   

9.
Time-dependent density functional theory (TDDFT) calculations on the photoabsorption process of the 11-cis retinal protonated Schiff base (PSB) chromophore show that the Franck-Condon relaxation of the first excited state of the chromophore involves a torsional twist motion of the beta-ionone ring relative to the conjugated retinyl chain. For the ground state, the beta-ionone ring and the retinyl chain of the free retinal PSB chromophore form a -40 degrees dihedral angle as compared to -94 degrees for the first excited state. The double bonds of the retinal are shorter for the fully optimized structure of the excited state than for the ground state suggesting a higher cis-trans isomerization barrier for the excited state than for the ground state. According to the present TDDFT calculations, the excitation of the retinal PSB chromophore does not primarily lead to a reaction along the cis-trans torsional coordinate at the C11-C12 bond. The activation of the isomerization center seems to occur at a later stage of the photo reaction. The results obtained at the TDDFT level are supported by second-order M?ller-Plesset (MP2) and approximate singles and doubles-coupled cluster (CC2) calculations on retinal chromophore models; the MP2 and CC2 calculations yield for them qualitatively the same ground state and excited-state structures as obtained in the density functional theory and TDDFT calculations.  相似文献   

10.
The effect of hydroxymethyl conformation (gg, gt, and tg rotamers about the C4-C5 bond) on the conformational energies and structural parameters (bond lengths, bond angles, bond torsions) of the 10 envelope forms of the biologically relevant aldopentofuranose, 2-deoxy-beta-D-erythro-pentofuranose (2-deoxy-D-ribofuranose) 2, has been investigated by ab initio molecular orbital calculations at the HF/6-31G level of theory. C4-C5 bond rotation induces significant changes in the conformational energy profile of 2 (2gt and 2tg exhibit one global energy minimum, whereas 2gg exhibits two nearly equivalent energy minima), and structural changes, especially those in bond lengths, are consistent with predictions based on previously reported vicinal, 1,3- and 1,4-oxygen lone pair effects. HF/6-31G-optimized envelope geometries of 2gg were re-optimized using density functional theory (DFT, B3LYP/6-31G), and the resulting structures were used in DFT calculations of NMR spin-spin coupling constants involving 13C (i.e., J(CH) and J(CC) over one, two, and three bonds) in 2gg according to methods described previously. The computed J-couplings were compared to those reported previously in 2gt to assess the effect of C4-C5 bond rotation on scalar couplings within the furanose ring and hydroxymethyl side chain. The results confirm prior predictions of correlations between 2J(CH), 3J(CH), 2J(CC) and 3J(CC), and ring conformation, and verify the usefulness of a concerted application of these couplings (both their magnitudes and signs) in assigning preferred ring and C4-C5 bond conformations in aldopentofuranosyl rings. The new calculated J-couplings in 2gg have particular relevance to related J-couplings in DNA (and RNA indirectly), where the gg rotamer, rather than the gt rotamer, is observed in most native structures. The effects of two additional structural perturbations on 2 were also studied, namely, deoxygenation at C5 (yielding 2,5-dideoxy-beta-D-erythro-pentofuranose 4) and methyl glycosidation at O1 (yielding methyl 2-deoxy-beta-D-erythro-pentofuranoside 5) at the HF/6-31G level. The conformational energy profile of 4 resembles that found for 2gt, not 2gg, indicating that 4 is an inappropriate structural mimic of the furanose ring in DNA. Glycosidation failed to induce differential stabilization of ring conformations containing an axial C1-O1 bond (anomeric effect), contrary to experimental data. The latter discrepancy indicates that either the magnitude of this differential stabilization depends on ring configuration or that solvent effects, which are neglected in these calculations, play a role in promoting this stabilization.  相似文献   

11.
Using density functional theory we have studied the structural properties of eleven C54 isomers that appear in the C60 fragmentation. We have evaluated the relative stability of the different isomers with respect the most stable one, which corresponds to the structure with the minimum number (four) of adjacent pentagons. On average, the length of a bond shared by pentagons and/or hexagons increases in the order hexagon-hexagon, hexagon-pentagon and pentagon-pentagon. However, we have found that the central bond in the confluence of four hexagons, i.e. a pyrene substructure, is anomalously large, becoming in some cases the largest one. We have also evaluated the nucleus-independent chemical shifts (NICS) at the center of every individual ring in the most stable isomers. For the chlorine derivatives, our calculations show that the favorite position for chlorine addition are the bonds shared by pentagons.  相似文献   

12.
AIM analysis was applied to study the changes in such topological parameters as the electron density at critical points of all the bonds of the molecule during the so-called nonadiabatic proton transfer in intramolecular hydrogen bonding in o-hydroxy aryl Schiff bases. Proton transfer is presented by a stepwise elongation and fixing of the hydroxyl bond with complete optimization of the rest of the parameters of the molecule by the B3LYP/6-311++G(d,p) method. A more detailed study of electron density changes at the critical points of the chelate and phenol rings in the stepwise proton-transfer process is presented. It was shown that the dependency of the electron density at the critical point of the chelate ring on tautomeric equilibrium is of a complicated character, whereas it is linear for the phenol ring. A complex study of the changes in the total electron density at the hydrogen bond, the quasi-aromatic ring, and in the whole molecule has been accomlished. The calculations of the intramolecular hydrogen bond by means of conformational and topological methods are discussed.  相似文献   

13.
Ab initio QM/MM dynamics simulation is employed to examine the stability of the tetrahedral intermediate during the deacylation step in elastase-catalyzed hydrolysis of a simple peptide. An extended quantum region includes the catalytic triad, the tetrahedral structure, and the oxyanion hole. The calculations indicate that the tetrahedral intermediate of serine proteases is a stable species on the picosecond time scale. On the basis of geometrical and dynamical properties, and in agreement with many experimental and theoretical studies, it is suggested that the crucial hydrogen bonds involved in stabilizing this intermediate are between Asp-102 and His-57 and between the charged oxygen of the intermediate and the backbone N-H group of Gly-193 in the oxyanion hole. The mobility of the imidazolium ring between O(w) and O(gamma), two of the oxygens of the tetrahedral structure, shows how the intermediate could proceed toward the product state without a "ring-flip mechanism", proposed earlier on the basis of NMR data. In addition to the proposed C(epsilon)(1)-H.O hydrogen bond between the imidazolium ring and the backbone carbonyl of Ser-214, we observe an alternative C(epsilon)(1)-H.O hydrogen bond with the backbone carbonyl of Thr-213, that can stabilize the intermediate during the imidazolium movement. Proton hopping occurs between Asp-102 and His-57 during the simulation. The proton is, however, largely localized on the nitrogen, and hence it does not participate in a low-barrier hydrogen bond. The study also suggests factors that may be implicated in product release: breaking the hydrogen bond of the charged oxygen with the backbone of Ser-195 in the oxyanion hole and a loop opening between residues 216-225 that enables the breaking of a hydrogen bond in subsite S(3).  相似文献   

14.
A high‐level ab initio Hartree‐Fock/Møller‐Plesset 2 and density functional theory quantum chemical calculations were performed on p‐chlorobenzaldehyde diperoxide energetic molecule to understand its bond topological, electrostatic, and energetic properties. The optimized molecular geometry for the basis set 6‐311G** exhibit chair diperoxide ring and planar aromatic side rings. Although the diperoxide ring bear same type of side rings, surprisingly, both the rings are almost perpendicular to each other, and the dihedral angle is 96.1°. The MP2 method predicts the O? O bond distance as ~1.466 Å. The charge density calculation reveals that the C? C bonds of chlorobenzaldehyde ring have rich electron density and the value is ~2.14 e Å?3. The maximum electron density of the O? O bonds does not lie along the internuclear axes; in view of this, a feeble density is noticed in the ring plane. The high negative values of laplacian of C? C bonds (approximately ?22.4 e Å?5) indicate the solidarity of these bonds, whereas it is found too small (approximately ?1.8 e Å?5 for MP2 calculation) in O? O bonds that shows the existence of high degree of bond charge depletion. The energy density in all the C? C bonds are found to be uniform. A high electronegative potential region is found at the diperoxide ring which is expected to be a nucleophilic attack area. Among the bonds, the O? O bond charge is highly depleted and it also has high bond kinetic energy density; in consequence of this, the molecular cleavage is expected to happen across these bonds when the material expose to any external stimuli such as heat or pressure treatment. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011  相似文献   

15.
The spectral and structural changes taking place in the course of the conversion of 1,2-benzisothiazol-3-(2H)-thione-1,1-dioxide (thiosaccharin) into a nitranion have been studied on the basis of both IR spectra and ab initio HF 6-31G(d) and BLYP 6-31G(d,p) force field calculations. The conversion causes nu(as)SO2 and nu(s)SO2 frequency decreases of 47 and 13 cm(-1), respectively, and other spectral changes. The nuC=S coordinate is strongly delocalized. The ab initio geometries of the isolated molecule and nitranion agree well with the single-crystal X-ray ones, determined for thiosaccharin and its sodium (potassium) monohydrate salts, respectively. The nitranionic charge is delocalized almost uniformly within the thiocarbonyl (0.29 e-), sulfonyl (0.24 e-), and phenylene (0.24 e-) groups, and the nitranionic center (0.23 e-).  相似文献   

16.
MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) quantum calculations are used to study the formamide-formic acid complex (FFAC), a system bound by two hydrogen bonds, N--H...O and O--H...O, that forms a bond ring at equilibrium. When the intermolecular separation between monomers R increases, this ring opens at a distance for which the weaker N--H...O bond breaks remaining the stronger O--H...O bond. The computational study characterizes that process addressing changes of interaction energy DeltaE, structure and properties of the electron density rho(r) as well as spatial distributions of rho(r), the electrostatic potential U(r), and the electron localization function eta(r). It is shown that the spatial derivatives of DeltaE, the topology of rho(r), and qualitative changes noticed in U(r) = 0 isocontours allow to identify a precise distance R for which one can say the N--H...O hydrogen bond has broken. Both levels of theory predict essentially the same changes of structure and electron properties associated to the process of breaking and virtually identical distances at which it takes place.  相似文献   

17.
Quantum chemical calculations of the structures and thermodynamics of homolytic dissociation of the central P-P and N-N bonds in tetrakis(disyl)diphosphine and tetrakis(di-tert-butylsilyl)hydrazine have been performed. The theory predicted negative standard enthalpies for homolytic bond dissociation in both cases, -71.0 and -108.4 kJ mol(-1) for the diphosphine and hydrazine, respectively, using the ONIOM (MP2/6-31+G*:B3LYP/3-21G*) level. The dissociation is accompanied by considerable structural changes in the radicals as compared to the corresponding fragments of the parent molecules, resulting in low dissociation enthalpies. The most pronounced changes in both radicals are the relaxation of bond angles in the substituents and a conformational change in the orientation of the substituent groups. In addition, the bis(di-tert-butylsilyl)aminyl radical displays a considerable increase in Si-N-Si angle and shortening of the Si-N bonds upon dissociation. These changes are not associated with any appreciable delocalisation of the lone electron, as the spin density is found from the B3LYP/3-21G* calculations to be largely concentrated on the nitrogen atom. It has been also shown that although the dissociation energies are low for both compounds, the intrinsic energies of the central bonds are still high, 140.6 kJ mol(-1) for the P-P bond in tetrakis(disyl)diphosphine and 490.6 kJ mol(-1) for the N-N bond in tetrakis(di-tert-butylsilyl)hydrazine, using the ONIOM method. The calculations predict that the dissociation of tetrakis(disyl)diphosphine would have negative free energy even without taking relaxation of the fragments into account, while the full potential of releasing about 306 kJ mol(-1) of energy stored in the ligands of tetrakis(di-tert-butylsilyl)hydrazine is only fully realised upon a considerable separation of the fragments.  相似文献   

18.
The antiaromaticity of fluorenylidene dications 1-5, which contain cyclic cationic substituents, has been examined using magnetic criteria, NICS and magnetic susceptibility, and by structural criteria, HOMA. The magnetic criteria, including proton chemical shifts, strongly support the antiaromaticity of the fluorenyl ring system of these dications. HOMA values are a very insensitive measure of structural effects in polycyclic ring systems because they reflect the inability of the fused ring systems to respond to changes in aromaticity/antiaromaticity. Finally, in these systems, the interaction between the ring systems appears to occur primarily through a type of hyperconjugation, as demonstrated by a decrease in the bond lengths for the bonds connecting the ring systems. In conjunction with the evaluation of magnetic effects, the quality of the calculation of (1)H and (13)C NMR shifts was assessed by comparison with experimental data. The calculation of (13)C NMR shifts was excellent in all methods examined, but the quality of (1)H NMR shifts was substantially poorer in calculations using the IGLO method, basis set DZ or II. The CSGT method gives a superior correlation between experimental and calculated (1)H NMR shifts.  相似文献   

19.
The nature of the 2e/12c bond and its conversion to a carbon-carbon single bond in phenalenyl dimers have prompted a great deal of interests recently. In this work, we theoretically investigated a series of π-stacking phenalenyl derivatives with 2e/12c bonding character by density functional theory (DFT) calculations to elucidate origin of this unusual bond conversion. Results show that bond-conversion of the phenalenyl dimer easily occurs at room-temperature both dynamically and thermodynamically. However, bond-conversion of hetero π-stacking adducts, in which the two center carbon atoms were substituted by boron and nitrogen atoms, respectively, is much more difficult, because the 2e/12c bond is stabilized by its charge transfer character. Consequently, the bond-conversion is an endothermic process, albeit with a low conversion barrier. Interestingly, Lewis acid-base interactions would be induced by substitution of the center nitrogen atom to phosphorus atom. The 2e/12c bond is further stabilized by 5.9 kcal mol−1 and its conversion is also thermodynamically unfavorable.  相似文献   

20.
NIR-FT Raman and FT-IR spectra of the crystallized biologically active molecule N,N′-diphenylguanidinium nitrate (DGN) have been recorded and analyzed using quantum chemical computations based on density functional theory. The extraordinary basicity and strong stability of this novel bioactive compound has been discussed as the consequence of resonance stabilization leading to Y-aromaticity and hydrogen bonding. This peculiar Y-delocalization character of DGN is well reflected in the optimized geometry and bond order (BO) calculations. The observance of the equality of C–N bond lengths in the protonated species indicates delocalization of the π-electron system. The spectroscopic and natural bonds orbital (NBO) analysis confirms the occurrence of strong network of inter molecular hydrogen bonds. The changes in electron density in the global minimum and in the energy of hyperconjugative interactions of DGN calculated by second order perturbation theory have been studied extensively in comparison with the values of the neutral species. The observed characteristic ring vibrations are well fit with the theoretical values calculated at B3LYP/6-31G* level.  相似文献   

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