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1.
2.
A new kind of aromatic trigonal bipyramidal MN3M (M=Be, B, Mg, Al, and Ca) species, with all real frequencies, is obtained at the MP2/6-311+G(3d) level. The nucleus-independent chemical shift values are -102.16 ppm for the N3 (3-) ring, and -74.09, -79.39, -65.06, -74.44, and -62.33 ppm (at the geometrical center of the trigonal bipyramid) for BeN3Be, BN3B, MgN3Mg, AlN3Al, and CaN3Ca, respectively. Molecular orbital analysis indicates that the regular triangular N3 (3-) ring and each MN3M species have three aromatic six-electron systems (pi, sigma(p), and sigma(s)) and exhibit threefold aromaticity. The CaN3Ca species has a very low vertical ionization energy of 3.64 eV at the CCSD(T)/6-311+G(3d) level, which is even lower than the ionization energy (3.9 eV) of the Cs atom. Therefore, CaN3Ca can be considered as a new superalkali species. A further study on the CaN3CaCl molecule confirms the superalkali characteristics of CaN3Ca. Two interesting phenomena are explored in the MN3M species: the delocalized electron cloud of the N3 subunit is elongated by two M cations, and the electron clouds of two M cations are distended by the N3 (3-) ring.  相似文献   

3.
The structures, energetics, and aromatic character of dicyclobuta[de,ij]naphthalene, 1, dicyclopenta[cd,gh]pentalene, 2, dihydrodicyclobuta[de,ij]naphthalene, 3, and dihydrocyclopenta[cd,gh]pentalene, 4, have been examined at the B3LYP/6-311++G//B3LYP/6-31G level of theory. All molecules are bowl-shaped, and the pentalene isomers, 2 and 4, are most stable. A comparison with other C(12)H(6) and C(12)H(8) isomers indicates that 2 is approximately 25 kcal/mol less stable than 1,5,9-tridehydro[12]annulene and 4 is approximately 100 kcal/mol higher in energy than acenaphthylene, both of which are synthetically accessible. The transition state structure for bowl-to-bowl inversion of 1 is planar (D(2)(h)()) and lies 30.9 kcal/mol higher in energy than the ground state; the transition state for inversion of 2 is C(2)(h)() and lies 46.6 kcal/mol higher in energy. Symmetry considerations, bond length alternations, and NICS values (a magnetic criterion) all indicate that the ground states of 1, 3, and 4 are very aromatic; however, HOMA values (a measure of bond delocalization) indicate that 3S and 4S are aromatic but that 1S is less so. NICS values for the ground state of 2 strongly indicate aromaticity; however, bond localization, symmetry, and HOMA values argue otherwise.  相似文献   

4.
Ab initio (MP2) and density functional theory (DFT) methods are used to examine a series of MN4 compounds, where M is an alkaline-earth cation (Mg2+, Ca2+, Sr2+, Ba2+), and N4(2-) is a six--electron ring. All pyramidal structures except MgN4 are the most energetically favored for all singlet MN4 systems considered here. For MgN4, the CS structure with dicoordinated Mg out of the N4 ring plane is the most stable of all. Among these systems, the pyramidal CaN4, SrN4, BaN4 and the planar C(S) structure containing dicoordinated Ba are stable as singlet molecules due to their significant isomerization or dissociation barriers (21.3-94.1 kcal/mol). Structural, natural bond orbital (NBO), and molecular orbital (MO) analyses indicate that the bonding in the BaN4 system has a larger covalent character as compared with other MN4 systems. In addition, substantial d character is found in the bonding of the MN4 (M = Ca2+, Sr2+, Ba2+) species.  相似文献   

5.
Intermolecular interactions involving aromatic pi-electron density are widely believed to be governed by the aromatic molecular quadrupole moment, Theta(zz). Arene-cation binding is believed to occur primarily with negative Theta(zz) aromatics, and arene-anion binding is believed to occur largely with positive Theta(zz) aromatics. We have performed quantum mechanical computations that show the cation binding of positive Theta(zz) aromatics and the anion binding of negative Theta(zz) aromatics is quite common in the gas phase. The pi-electron density of hexafluorobenzene, the prototypical positive Theta(zz ) aromatic (experimental Theta(zz) = 9.5 +/- 0.5 DA), has a Li+ binding enthalpy of -4.37 kcal/mol at the MP2(full)/6-311G**level of theory. The RHF/6-311G** calculated Theta(zz) value of 1,4-dicyanobenzene is +11.81 DA, yet it has an MP2(full)/6-311G** Li+ binding enthalpy of -12.65 kcal/mol and a Na+ binding enthalpy of -3.72 kcal/mol. The pi-electron density of benzene, the prototypical negative Theta(zz) aromatic (experimental Theta(zz) = -8.7 +/- 0.5 DA), has a F- binding enthalpy of -5.51 kcal/mol. The RHF/6-311G** calculated Theta(zz) of C6H2I4 is -10.45 DA, yet it has an MP2(full)/6-311++G** calculated F- binding enthalpy of -20.13 kcal/mol. Our results show that as the aromatic Theta(zz) value increases the cation binding enthalpy decreases; a plot of cation binding enthalpies versus aromatic Theta(zz) gives a line of best of fit with R2 = 0.778. No such correlation exists between the aromatic Theta(zz) value and the anion binding enthalpy; the line of best fit has R2 = 0.297. These results are discussed in terms of electrostatic and polarizability contributions to the overall binding enthalpies.  相似文献   

6.
[structure: see text] While the total aromatic stabilization energies (ASE) of the [n]annulenes, from C(6)H(6) to C(66)H(66), converge to ca. 22 kcal/mol, the ASEs per pi-electron decrease markedly. Bond length alternation (which depends on the theoretical level) only reduces stabilization somewhat but influences the magnetic properties (NICS, proton chemical shifts, and magnetic susceptibilities) considerably. Nevertheless, these magnetic criteria, when based on the most realistic structures, agree that the aromaticities of the larger annulenes decrease and then nearly vanish.  相似文献   

7.
Quantitative evidence for the existence of aromaticity involving the d orbitals of transition metals is provided for the first time. The doubly bridged square planar (D(4)(h)()) coinage metal clusters (M(4)Li(2), M = Cu (1), Ag (2), and Au (3)) are characterized as aromatic by their substantial nucleus independent chemical shifts (NICS) values in the centers (-14.5, -14.1, and -18.6, respectively). Nevertheless, the participation of p orbitals in the bonding (and cyclic electron delocalization) of 1-3 is negligible. Instead, these clusters benefit strongly from the delocalization of d and to some extent s orbitals. The same conclusion applies to Tsipis and Tsipis' H-bridged D(4)(h)() Cu(4)H(4) ring (4). Canonical MO-NICS analysis of structures 1-3 shows the total diatropic d orbital contributions to the total NICS to be substantial, although the individual contributions of the five sets of filled d orbitals vary. The d orbital aromaticity of Cu(4)Li(2) also is indicated by its atomization energy, 243.2 kcal/mol, which is larger than Boldyrev's doubly (sigma and pi) aromatic Al(4)Li(2) (215.9 kcal/mol).  相似文献   

8.
The total electronic energy and nucleus-independent chemical shift (NICS) of 95 isomers of N-confused porphyrin (NCP: normal porphyrin (N(0)CP), singly N-confused porphyrin (N(1)CP), doubly N-confused porphyrin (N(2)CP), triply N-confused porphyrin (N(3)CP), and fully N-confused porphyrin (N(4)CP)) have been calculated by the density functional theory (DFT) method. The stability of NCP decreased by increasing the number of confused pyrrole rings. Namely, the relative energies of the most stable isomers in each confusion level increased in a stepwise manner approximately by +18 kcal/mol: 0 (N(0)CP1), +17.147 (N(1)CP2), +37.461 (N(2)CPb3), +54.031 (N(3)CPd6), and +65.636 kcal/mol (N(4)CPc8). In this order, the mean plane deviation of these isomers increased from 0.000 to 0.123, 0.170, 0.215, and 0.251 A, respectively. The unusual tautomeric forms of pyrrole ring with an sp(3)-carbon were found in the stable forms of N(3)CP and N(4)CP. The NICS values at the mean position of the 24 core atoms were nearly the same for the most aromatic isomers regardless of the confusion level: -15.1280 (N(0)CP1), -13.8493 (N(1)CP2), -13.7267 (N(2)CPd1), -11.7723 (N(3)CPb5), and -13.6224 ppm (N(4)CPa6). The positive correlation between aromaticity and stability was inferred from the plots of NICS and the relative energy of NCP for N(0)CP, N(1)CP, and trans-N(2)CP. On the other hand, the correlation was negative for cis-N(2)CP, N(3)CP, and N(4)CP isomers.  相似文献   

9.
10.
The complex of Na(+) with phenylalanine (Phe) is a prototype for the participation of cation-pi interactions in metal-ion binding to biological molecules. A recent comparison of this complex with the Na(+)/alanine (Na(+)/Ala) counterpart suggested only a small contribution of the phenyl ring interaction to binding, casting doubt on the extent of the cation-pi effect. The present work reexamines this thermochemistry using ligand-exchange equilibrium measurements in the Fourier transform ion cyclotron resonance (FT-ICR) ion trapping mass spectrometer. An increment of 7 +/- 2 kcal mol(-1) was found in the Ala/Phe comparison of binding enthalpies, confirming the importance of cation-pi binding enhancement in the Phe case. Absolute Na(+) binding enthalpies of 38 +/- 2 and 45 +/- 2 kcal mol(-1) were assigned for Ala and Phe, respectively, using pyridine as the thermochemical reference ligand. All of these results were supported by quantum calculations using both density functional and Hartree-Fock/MP2 methods, improved in several respects over previous calculations. Alanine methyl ester (AlaMe) was also observed, and found to have an Na(+) ion affinity larger by 2.3 kcal mol(-1) than Ala. New, lower energy conformations of neutral Phe were discovered in the computations.  相似文献   

11.
12.
A detailed theoretical investigation of the [H,Si,C(2),N] potential energy surfaces including 28 minimum isomers and 65 interconversion transition states is reported at the Gaussian-3//B3LYP/6-31G(d) level. Generally, the triplet species lie energetically higher than the singlet ones. The former three low-lying isomers are linear HCCNSi 1 (0.00 kcal/mol), branched SiC(H)CN 12 (7.09 kcal/mol), and bent HNCCSi 7 (14.22 kcal/mol), which are separated by rather high barriers from each other and are kinetically very stable with the least conversion barriers of 32.6-70.5 kcal/mol. Two energetically high-lying isomers HCNCSi 3 (42.99 kcal/mol) and SiC(H)NC 13 (36.05 kcal/mol) are also kinetically stable with a barrier of 49.19 and 21.42 kcal/mol, respectively. Additionally, five high-lying isomers, that is, three chainlike isomers, HCCSiN 2 (55.17), HCSiNC 6 (47.80), HSiNCC 11 (78.83), and one three-membered ring isomer HN-cSiCC 19 (51.21), and one four-membered ring isomer cSiCN(H)C 27 (50.6 kcal/mol), are predicted to each have lower conversion barriers of 12-18 kcal/mol and can be considered as meta-stable species. All of the predicted 10 isomers could exist as stable or meta-stable intermediates under suitable conditions. Finally, the structural and bonding analysis indicate that the [H,Si,C(2),N] molecule contains various properties that are of chemical interest (e.g., silylene, SiC triple bonding, and conjugate SiN triple bonding and CC triple bonding, charge-transfer specie, planar aromatic specie, cumulate double bonding). This is the first detailed theoretical study on the potential energy surfaces of the series of hydrogenated Si,C,C,N-containing molecules. The knowledge of the present monohydrogenated SiC(2)N isomerism could provide useful information for more highly hydrogenated or larger Si,C(2),N-containing species.  相似文献   

13.
The magnetic properties of a series of inorganic saturated rings, (SiH2)n, (GeH2)n, (NH)n, (PH)n, (AsH)n, On, Sn, and Sen (n = 3-6), exhibit zigzag behavior with ring size resembling that of aromatic and antiaromatic Hückel pi-systems and (CH2)n rings. Computed GIAO-SCF nucleus-independent chemical shifts (NICS) and localized (LMO) NICS analysis indicate that the sigma-ring electrons are chiefly responsible for this zigzag behavior. This evidence for sigma-aromaticity is further supported by theoretical strain energy (TSE). The Hückel 4n + 2/4n aromaticity/antiaromaticity rule for pi-electron systems applies well to the smaller saturated rings.  相似文献   

14.
Six water molecules have been used for microsolvation to outline a hydrogen bonded network around complexes of ethylene epoxide with nucleotide bases adenine (EAw), guanine (EGw) and cytosine (ECw). These models have been developed with the MPWB1K-PCM/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) level of DFT method and calculated S(N)2 type ring opening of the epoxide due to amino group of the nucleotide bases, viz. the N6 position of adenine, N2 position of guanine and N4 position of cytosine. Activation energy (E(act)) for the ring opening was found to be 28.06, 28.64, and 28.37 kcal mol(-1) respectively for EAw, EGw and ECw. If water molecules were not used, the reactions occurred at considerably high value of E(act), viz. 53.51 kcal mol(-1) for EA, 55.76 kcal mol(-1) for EG and 56.93 kcal mol(-1) for EC. The ring opening led to accumulation of negative charge on the developing alkoxide moiety and the water molecules around the charge localized regions showed strong hydrogen bond interactions to provide stability to the intermediate systems EAw-1, EGw-1 and ECw-1. This led to an easy migration of a proton from an activated water molecule to the alkoxide moiety to generate a hydroxide. Almost simultaneously, a proton transfer chain reaction occurred through the hydrogen bonded network of water molecules and resulted in the rupture of one of the N-H bonds of the quaternized amino group. The highest value of E(act) for the proton transfer step of the reaction was 2.17 kcal mol(-1) for EAw, 2.93 kcal mol(-1) for EGw and 0.02 kcal mol(-1) for ECw. Further, the overall reaction was exothermic by 17.99, 22.49 and 13.18 kcal mol(-1) for EAw, EGw and ECw, respectively, suggesting that the reaction is irreversible. Based on geometric features of the epoxide-nucleotide base complexes and the energetics, the highest reactivity is assigned for adenine followed by cytosine and guanine. Epoxide-mediated damage of DNA is reported in the literature and the present results suggest that hydrated DNA bases become highly S(N)2 active on epoxide systems and the occurrence of such reactions can inflict permanent damage to the DNA.  相似文献   

15.
The electronic structure and bonding situation in 21 metallabenzenes (metal=Os, Ru, Ir, Rh, Pt, and Pd) were investigated at the DFT level (BP86/TZ2P) by using an energy decomposition analysis (EDA) of the interaction energy between various fragments. The aim of the work is to estimate the strength of the pi bonding and the aromatic character of the metallacyclic compounds. Analysis of the electronic structure shows that the metallacyclic moiety has five occupied pi orbitals, two with b1 symmetry and three with a2 symmetry, which describe the pi-bonding interactions. The metallabenzenes are thus 10 pi-electron systems. This holds for 16-electron and for 18-electron complexes. The pi bonding in the metallabenzenes results mainly from the b1 contribution, but the a2 contribution is not negligible. Comparison of the pi-bonding strength in the metallacyclic compounds with acylic reference molecules indicates that metallabenzenes should be considered as aromatic compounds whose extra stabilization due to aromatic conjugation is weaker than in benzene. The calculated aromatic stabilization energies (ASEs) are between 8.7 kcal mol(-1) for 13 and 37.6 kcal mol(-1) for 16 which is nearly as aromatic as benzene (ASE=42.5 kcal mol(-1)). The classical metallabenzene model compounds 1 and 4 exhibit intermediate aromaticity with ASE values of 33.4 and 17.6 kcal mol(-1). The greater stability of the 5d complexes compared with the 4d species appears not to be related to the strength of pi conjugation. From the data reported here there is no apparent trend or pattern which indicates a correlation between aromatic stabilization and particular ligands, metals, coordination numbers or charge. The lower metal-C5H5 binding energy of the 4d complexes correlates rather with weaker sigma-orbital interactions.  相似文献   

16.
It has been assumed that the pi-electrons of aromatic residues in the catalytic sites of triterpene cyclases stabilize the cationic intermediates formed during the polycyclization cascade of squalene or oxidosqualene, but no definitive experimental evidence has been given. To validate this cation-pi interaction, natural and unnatural aromatic amino acids were site-specifically incorporated into squalene-hopene cyclase (SHC) from Alicyclobacillus acidocaldarius and the kinetic data of the mutants were compared with that of the wild-type SHC. The catalytic sites of Phe365 and Phe605 were substituted with O-methyltyrosine, tyrosine, and tryptophan, which have higher cation-pi binding energies than phenylalanine. These replacements actually increased the SHC activity at low temperature, but decreased the activity at high temperature, as compared with the wild-type SHC. This decreased activity is due to the disorganization of the protein architecture caused by the introduction of the amino acids more bulky than phenylalanine. Then, mono-, di-, and trifluorophenylalanines were incorporated at positions 365 and 605; these amino acids reduce cation-pi binding energies but have van der Waals radii similar to that of phenylalanine. The activities of the SHC variants with fluorophenylalanines were found to be inversely proportional to the number of the fluorine atoms on the aromatic ring and clearly correlated with the cation-pi binding energies of the ring moiety. No serious structural alteration was observed for these variants even at high temperature. These results unambiguously show that the pi-electron density of residues 365 and 605 has a crucial role for the efficient polycyclization reaction by SHC. This is the first report to demonstrate experimentally the involvement of cation-pi interaction in triterpene biosynthesis.  相似文献   

17.
Cation-pi interactions between amino acid side chains are increasingly being recognized as important structural and functional features of proteins and other biomolecules. Although these interactions have been found in static protein structures, they have not yet been detected in dynamic biomolecular systems. We determined, by (1)H NMR spectroscopic titrations, the energies of cation-pi interactions of the amino acid derivative AcLysOMe (1) with AcPheOEt (2) and with AcTyrOEt (3) in aqueous and three organic solvents. The interaction energy is substantial; it ranges from -2.1 to -3.4 kcal/mol and depends only slightly on the dielectric constant of the solvent. To assess the effects of auxiliary interactions and structural preorganization on formation of cation-pi interactions, we studied these interactions in the association of pentapeptides. Upon binding of the positively-charged peptide AcLysLysLysLysLysNH(2) (5) to the negatively-charged partner AcAspAspXAspAspNH(2) (6), in which X is Leu (6a), Tyr (6b), and Phe (6c), multiple interactions occur. Association of the two pentapeptides is dynamic. Free peptides and their complex are in fast exchange on the NMR time-scale, and 2D (1)H ROESY spectra of the complex of the two pentapeptides do not show intermolecular ROESY peaks. Perturbations of the chemical shifts indicated that the aromatic groups in peptides 6b and 6c were affected by the association with 5. The association constants K(A) for 5 with 6a and with 6b are nearly equal, (4.0 +/- 0.7) x 10(3) and (5.0 +/- 1.0) x 10(3) M(-)(1), respectively, while K(A) for 5 with 6c is larger, (8.3 +/- 1.3) x 10(3) M(-)(1). Molecular-dynamics (MD) simulations of the pentapeptide pairs confirmed that their association is dynamic and showed that cation-pi contacts between the two peptides are stereochemically possible. A transient complex between 5 and 6 with a prominent cation-pi interaction, obtained from MD simulations, was used as a template to design cyclic peptides C(X) featuring persistent cation-pi interactions. The cyclic peptide C(X) had a sequence in which X is Tyr, Phe, and Leu. The first two peptides do, but the third does not, contain the aromatic residue capable of interacting with a cationic Lys residue. This covalent construct offered conformational stability over the noncovalent complexes and allowed thorough studies by 2D NMR spectroscopy. Multiple conformations of the cyclic peptides C(Tyr) and C(Phe) are in slow exchange on the NMR time-scale. In one of these conformations, cation-pi interaction between Lys3 and Tyr9/Phe9 is clearly evident. Multiple NOEs between the side chains of residues 3 and 9 are observed; chemical-shift changes are consistent with the placement of the side chain of Lys3 over the aromatic ring. In contrast, the cyclic peptide C(Leu) showed no evidence for close approach of the side chains of Lys3 and Leu9. The cation-pi interaction persists in both DMSO and aqueous solvents. When the disulfide bond in the cyclic peptide C(Phe) was removed, the cation-pi interaction in the acyclic peptide AC(Phe) remained. To test the reliability of the pK(a) criterion for the existence of cation-pi interactions, we determined residue-specific pK(a) values of all four Lys side chains in all three cyclic peptides C(X). While NOE cross-peaks and perturbations of the chemical shifts clearly show the existence of the cation-pi interaction, pK(a) values of Lys3 in C(Tyr) and in C(Phe) differ only marginally from those values of other lysines in these dynamic peptides. Our experimental results with dynamic peptide systems highlight the role of cation-pi interactions in both intermolecular recognition at the protein-protein interface and intramolecular processes such as protein folding.  相似文献   

18.
Geometries, energies and magnetic shieldings are reported at the ab initio B3LYP/6-31G* level for the phenylene cluster C120 (archimedene) and eight phenylene-based hydrocarbon bowls consisting of four-, six-, and ten-membered rings. The six-membered rings are branched, angular, or terminal. The latter are the most aromatic, based upon NICS criteria and lack of substantial bond alternation. At the other extreme are branched rings, having less negative NICS values. Four-membered rings, except those on a rim, are nearly square. Regularities are found in the ab initio energies, heats of formation (deltaH(o)f), and strain energies relative to those of hypothetical planar acyclic analogues. The bowls appear to have little aromatic character, and their interiors are but slightly shielded. Archimedene, with deltaH(o)f = 2191 kcal/mol, has energetic and structural properties akin to those of phenylene-based bowls.  相似文献   

19.
The gas phase and solvent dependent preference of the tautomerization between 2-pyridinethiol (2SH) and 2-pyridinethione (2S) has been assessed using variable temperature Fourier transform infrared (FTIR) experiments, as well as ab initio and density functional theory computations. No spectroscopic evidence (nu(S)(-)(H) stretch) for 2SH was observed in toluene, C(6)D(6), heptane, or methylene chloride solutions. Although, C(s)() 2SH is 2.61 kcal/mol more stable than C(s)() 2S (CCSD(T)/cc-pVTZ//B3LYP/6-311+G(3df,2p)+ZPE), cyclohexane solvent-field relative energies (IPCM-MP2/6-311+G(3df,2p)) favor 2S by 1.96 kcal/mol. This is in accord with the FTIR observations and in quantitative agreement with the -2.6 kcal/mol solution (toluene or C(6)D(6)) calorimetric enthalpy for the 2S/2SH tautomerization favoring the thione. As the intramolecular transition state for the 2S, 2SH tautomerization (2TS) lies 25 (CBS-Q) to 30 kcal/mol (CCSD/cc-pVTZ) higher in energy than either tautomer, tautomerization probably occurs in the hydrogen bonded dimer. The B3LYP/6-311+G(3df,2p) optimized C(2) 2SH dimer is 10.23 kcal/mol + ZPE higher in energy than the C(2)(h)() 2S dimer and is only 2.95 kcal/mol + ZPE lower in energy than the C(2) 2TS dimer transition state. Dimerization equilibrium measurements (FTIR, C(6)D(6)) over the temperature range 22-63 degrees C agree: K(eq)(298) = 165 +/- 40 M(-)(1), DeltaH = -7.0 +/- 0.7 kcal/mol, and DeltaS = -13.4 +/- 3.0 cal/(mol deg). The difference between experimental and B3LYP/6-311+G(3df,2p) [-34.62 cal/(mol deg)] entropy changes is due to solvent effects. The B3LYP/6-311+G(3df,2p) nucleus independent chemical shifts (NICS) are -8.8 and -3.5 ppm 1 A above the 2SH and 2S ring centers, respectively, and the thiol is aromatic. Although the thione is not aromatic, it is stabilized by the thioamide resonance. In solvent, the large 2S dipole, 2-3 times greater than 2SH, favors the thione tautomer and, in conclusion, 2S is thermodynamically more stable than 2SH in solution.  相似文献   

20.
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