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1.
B3LYP/6-311+G** calculations on alkali metal ion (Li+ and Na+) complexation with corannulene and sumanene indicate stronger binding compared to [5]-radialene or benzene. The dependence of binding to the convex and concave site is marginal, albeit the preference was consistent for convex binding in the range of 1-4 kcal/mol. The bowl-to-bowl inversion barriers are only marginally affected, below 2 kcal/mol, by metal ion complexation.  相似文献   

2.
Density functionals with long‐range and/or empirical dispersion corrections, including LC‐ωPBE, B97‐D, ωB97X‐D, M06‐2X, B2PLYP‐D, and mPW2PLYP‐D functionals, are assessed for their ability to describe the conformational preferences of Ac‐Ala‐NHMe (the alanine dipeptide) and Ac‐Pro‐NHMe (the proline dipeptide) in the gas phase and in water, which have been used as prototypes for amino acid residues of peptides. For both dipeptides, the mean absolute deviation (MAD) is estimated to be 0.22–0.40 kcal/mol in conformational energy and 2.0–3.2° in torsion angles ? and ψ using these functionals with the 6‐311++G(d,p) basis set against the reference values calculated at the MP2/aug‐cc‐pVTZ//MP2/aug‐cc‐pVDZ level of theory in the gas phase. The overall performance is obtained in the order B2PLYP‐D ≈ mPW2PLYP‐D > ωB97X‐D ≈ M06‐2X > MP2 > LC‐ωPBE > B3LYP with the 6–311++G(d,p) basis set. The SMD model at the M06‐2X/6‐31+G(d) level of theory well reproduced experimental hydration free energies of the model compounds for backbone and side chains of peptides with MADs of 0.47 and 4.3 kcal/mol for 20 neutral and 5 charged molecules, respectively. The B2PLYP‐D/6‐311++G(d,p)//SMD M06‐2X/6‐31+G(d) level of theory provides the populations of backbone and/or prolyl peptide bond for the alanine and proline dipeptides in water that are consistent with the observed values. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010  相似文献   

3.
We have applied the multicoefficient density functional theory (MC‐DFT) to four recent Minnesota functionals, including M06‐2X, M08‐HX, M11, and MN12‐SX on the performance of thermochemical kinetics. The results indicated that the accuracy can be improved significantly using more than one basis set. We further included the SCS‐MP2 energies into MC‐DFT, and the resulting mean unsigned errors (MUEs) decreased by approximately 0.3 kcal/mol for the most accurate basis set combinations. The M06‐2X functional with the simple [6–311+G(d,p)/6–311+G(2d,2p)] combination gave the best performance/cost ratios for the MC‐DFT and MC‐SCS‐MP2|MC‐DFT methods with MUE of 1.58 and 1.22 kcal/mol, respectively. © 2014 Wiley Periodicals, Inc.  相似文献   

4.
Corannulene dimers made up of corannulene monomers with different curvature and substituents were studied using M06-2X, B97D and ωB97XD functionals and 6-31+G* basis set. Corannulene molecules were substituted with five alternating Br, Cl, CH(3), C(2)H or CN units. Geometric results showed that substituents gave rise to small changes in the curvature of corannulene bowls. So, there was not a clear relationship between the curvature of bowls and the changes on interaction energy generated by addition of substituents in the bowl. Electron withdrawing substituents gave rise to a more positive molecular electrostatic potential (MEP) of the bowl, which was able to get a strong interaction with the negative MEP at the surface of a fullerene. Substitution with CN caused the largest effect, giving rise to the most positive MEP and to a large interaction energy of -24.64 kcal mol(-1), at the ωB97XD/6-31+G* level. Dispersive effects must be taken into account to explain the catching ability of the different substituted corannulenes. For unsubstituted dimers, calculations with DFT-D methods employing ωB97XD and B97D functionals led to similar results to those previously reported at the SCS-MP2/cc-pVTZ level for corannulene dimers (A. Sygula and S. Saeb?, Int. J. Quant. Chem., 2009, 109, 65). In particular, the ωB97XD functional led to a difference of only 0.35 kcal mol(-1), regarding MP2 interaction energy for corannulene dimers. On the other hand, the M06-2X functional showed a general considerable underestimation of interaction energies. This functional worked quite well to study trends, but not to obtain absolute interaction energies.  相似文献   

5.
The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 48 hydrogen‐bonded amide–thymine and amide–uracil dimers are evaluated from the analytic potential energy function established in our lab recently. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the BSSE correction. For all the 48 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 46 dimers, only two differences are larger than 0.50 kcal/mol and the largest one is only 0.60 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.050 Å for all the 48 dimers. The analytic potential energy function is further applied to four more complicated hydrogen‐bonded amide–base systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded amide–base dimers quickly and accurately. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011  相似文献   

6.
A computational modeling of the protonation of corannulene at B3LYP/6-311G(d,p)//B3LYP/6-311G(d,p) and of the binding of lithium cations to corannulene at B3LYP/6-311G(d,p)//B3LYP/6-31G(d,p) has been performed. A proton attaches preferentially to one carbon atom, forming a sigma-complex. The isomer protonated at the innermost (hub) carbon has the best total energy. Protonation at the outermost (rim) carbon and at the intermediate (bridgehead rim) carbon is less favorable by ca. 2 and 14 kcal mol(-)(1), respectively. Hydrogen-bridged isomers are transition states between the sigma-complexes; the corresponding activation energies vary from 10 to 26 kcal mol(-)(1). With an empirical correction obtained from calculations on benzene, naphthalene, and azulene, the best estimate for the proton affinity of corannulene is 203 kcal mol(-)(1). The lithium cation positions itself preferentially over a ring. There is a small energetic preference for the 6-ring over the 5-ring binding (up to 2 kcal mol(-)(1)) and of the convex face over the concave face (3-5 kcal mol(-)(1)). The Li-bridged complexes are transition states between the pi-face complexes. Movement of the Li(+) cation over either face is facile, and the activation energy does not exceed 6 kcal mol(-)(1) on the convex face and 2.2 kcal mol(-)(1) on the concave face. In contrast, the transition of Li(+) around the corannulene edge involves a high activation barrier (24 kcal mol(-)(1) with respect to the lowest energy pi-face complex). An easier concave/convex transformation and vice versa is the bowl-to-bowl inversion with an activation energy of 7-12 kcal mol(-)(1). The computed binding energy of Li(+) to corannulene is 44 kcal mol(-)(1). Calculations of the (7)Li NMR chemical shifts and nuclear independent chemical shifts (NICS) have been performed to analyze the aromaticity of the corannulene rings and its changes upon protonation.  相似文献   

7.
Theoretical calculations were performed on the 1,3-dipolar cycloaddition reactions of 24 1,3-dipoles with ethylene and acetylene. The 24 1,3-dipoles are of the formula X≡Y(+)-Z(-) (where X is HC or N, Y is N, and Z is CH(2), NH, or O) or X═Y(+)-Z(-) (where X and Z are CH(2), NH, or O and Y is NH, O, or S). The high-accuracy G3B3 method was employed as the reference. CBS-QB3, CCSD(T)//B3LYP, SCS-MP2//B3LYP, B3LYP, M06-2X, and B97-D methods were benchmarked to assess their accuracies and to determine an accurate method that is practical for large systems. Several basis sets were also evaluated. Compared to the G3B3 method, CBS-QB3 and CCSD(T)/maug-cc-pV(T+d)Z//B3LYP methods give similar results for both activation and reaction enthalpies (mean average deviation, MAD, < 1.5 kcal/mol). SCS-MP2//B3LYP and M06-2X give small errors for the activation enthalpies (MAD < 1.5 kcal/mol), while B3LYP has MAD = 2.3 kcal/mol. SCS-MP2//B3LYP and B3LYP give the reasonable reaction enthalpies (MAD < 5.0 kcal/mol). The B3LYP functional also gives good results for most 1,3-dipoles (MAD = 1.9 kcal/mol for 17 common 1,3-dipoles), but the activation and reaction enthalpies for ozone and sulfur dioxide are difficult to calculate by any of the density functional methods.  相似文献   

8.
Ab initio HF/6-31+G*, MP2/6-31+G*, B3LYP/6-31+G* level calculations have been performed on HSe-NH2 to estimate the Se-N rotational barriers and N-inversion barriers. Two conformers have been found withsyn andanti arrangement of the NH2 hydrogens with respect to Se-H bond. The N inversion barriers in selenamide are 1.65, 2.47, 1.93 kcal/mol and the Se-N rotational barriers are 6.58, 6.56 and 6.12 kcal/mol respectively at HF/6-31+G*, MP2/6-31+G* and B3LYP/6-31+G* levels respectively. The nNΣ *Se-H negative hyperconjugation is found to be responsible for the higher rotational barriers.  相似文献   

9.
The mechanisms and kinetics of the gas phase reactions that the hydrogen atom in formyl uoride (FCHO) abstracted by OH in the presence of water, formic acid (FA), or sulfuric acid (SA) are theoretically investigated at the CCSD(T)/6-311++G(3df, 3pd)//M06-2X/6-311++G(3df, 3pd) level of theory. The calculated results show that the barriers of the transition states involving catalysts are lowered to -2.89, -6.25, and -7.76 kcal/mol from 3.64 kcal/mol with respect to the separate reactants, respectively, which re ects that those catalysts play an important role in reducing the barrier of the hydrogen abstraction reaction of FCHO with OH. Additionally, using conventional transition state theory with Eckart tun-neling correction, the kinetic data demonstrate that the entrance channel X FCHO+OH (X=H2O, FA, or SA) is signi cantly more favorable than the pathway X OH+FCHO. More-over, the rate constants of the reactions of FCHO with OH radical with H2O, FA, or SA introduced are computed to be smaller than that of the naked OH+FCHO reaction because the concentration of the formed X FCHO or X OH complex is quite low in the atmosphere.  相似文献   

10.
Ab initio MP2 level of theory in conjunction with three basis sets of a triple-zeta quality was applied to study the molecular geometry and stability of the H2CO... HF complex. An interaction energy predicted for this system at the highest, MP4(SDTQ)/6-311 + +G(2df, 2pd)//MP2/6-311 + +G(2df, 2pd), level corrected for the BSSE and ZPE contributions amounts to -4.85 kcal/ mol. BSSE contributes significantly to the interaction energies at all applied levels. Reliable MP2/ 6-311 + +G(2df, 2pd) level harmonic vibrational frequencies, IR intensities, and the predicted isotopic shifts upon deuteration and18O substitution are presented in order to facilitate experimental studies on the IR spectrum of the title complex.  相似文献   

11.
The effect of the parent basis set on the basis set superposition error caused by bond functions is investigated systematically. An important difference between BSSE at the SCF and correlated levels is pointed out. Three new basis sets are defined, denoted 6-311 + G(d,p)B, 6-311 + G(2d,p)B, and 6-311 + G(2df,p)B. BSSE for the first-row hydrides seems to increase uniformly with increasing atomic number of the central atom. Expansion of the valence part of the basis set from 6-31G to 6-311G, as well as adding f functions, has a significant effect on the BSSE. Additional BSSEs incurred by bond functions are less than or equal to 1 kcal/mol for the 6-311 + G(2df,p)B basis set. For the dissociation energies of the first-row hydride species, agreement with experiment within only a few kcal/mol can be obtained even without resorting to isogyric reaction cycles. For high-quality calculations, adding bond functions seems to have definite advantages over expanding the polarization space beyond the [2d1f] level.  相似文献   

12.
The addition of primary, secondary, and tertiary alkyl radicals to single wall carbon nanotubes (SWCNTs) was studied by means of dispersion corrected density functional theory. The PBE, B97‐D, M06‐L, and M06‐2X functionals were used. Consideration of Van der Waals interactions is essential to obtain accurate addition energies. In effect, the enthalpy changes at 298 K, for the addition of methyl, ethyl, isopropyl, and tert‐butyl radicals onto a (5,5) SWCNT are: ?25.7, ?25.1, ?22.4, and ?16.6 kcal/mol, at the M06‐2X level, respectively, whereas at PBE/6‐31G* level they are significantly lower: ?25.0, ?19.0, ?16.7, and ?5.0 kcal/mol respectively. Although the binding energies are small, the attached alkyl radicals are expected to be stable because of the large desorption barriers. The importance of nonbonded interactions was more noticeable as we moved from primary to tertiary alkyl radicals. Indeed, for the tert‐butyl radical, physisorption onto the (11,0) SWCNT is preferred rather than chemisorption. The bond dissociation energies determined for alkyl radicals and SWCNT follow the trend suggested by the consideration of radical stabilization energies. However, they are in disagreement with some degrees of functionalization observed in recent experiments. This discrepancy would stem from the fact that for some HiPco nanotubes, nonbonded interactions with alkyl radicals are stronger than covalent bonds. © 2012 Wiley Periodicals, Inc.  相似文献   

13.
The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 20 hydrogen‐bonded amide–base dimers are evaluated from the analytic potential energy function established in our laboratory recently. The analytic potential energy function is used to calculate the N? H···N, N? H···O?C, C? H···N, and C? H···O?C dipole–dipole attractive interaction energies and C?O···O?C, N? H···H? N, and N? H···H? C dipole–dipole repulsive interaction energies in the 20 dimers composed of DNA bases adenine, guanine, cytosine, or thymine and peptide amide. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6‐311+G** calculations by including the basis set superposition error (BSSE) correction. For all the 20 dimers, the analytic potential energy function yields the binding energies of the MP2/6‐311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 19 dimers, only one difference is larger than 0.50 kcal/mol and the difference is only 0.61 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6‐311+G** with BSSE correction within the error limits of 0.030 Å for all the 20 dimers. The analytic potential energy function is further applied to four more complicated DNA base‐peptide amide systems involving amino acid side chain and β‐sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen‐bonded peptide amide–DNA base dimers quickly and accurately. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011  相似文献   

14.
A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model chemistry yields MAD=0.68 kcal/mol, which represents a huge improvement over plain B3LYP/6-31G* (MAD=2.3 kcal/mol). Application of gCP-corrected B97-D3 and HF-D3 on a set of large protein-ligand complexes prove the robustness of the method. Analytical gCP gradients make optimizations of large systems feasible with small basis sets, as demonstrated for the inter-ring distances of 9-helicene and most of the complexes in Hobza's S22 test set. The method is implemented in a freely available FORTRAN program obtainable from the author's website.  相似文献   

15.
The conformational free energies for some 2-substituted butanes where X = F, Cl, CN, and CCH were calculated using G3-B3, CBS-QB3, and CCSD(T)/6-311++G(2d,p) as well as other theoretical levels. The above methods gave consistent results with free energies relative to the trans conformers as follows: X = CCH, g+ = 0.77 +/- 0.05 kcal/mol. g- = 0.88 +/- 0.05 kcal/mol; X = CN, g+ = 0.85 +/- 0.05 kcal/mol, g- = 0.75 +/- 0.05 kcal/mol; X = Cl, g+ = 0.70 +/- 0.05 kcal/ml, g- = 0.80 +/- 0.05 kcal/mol; and X = F, g+ = 0.53 +/- 0.05 kcal/mol, g- = 0.83 +/- 0.05 kcal/mol. The conformational free energies also were estimated using the observed liquid phase IR spectra and intensities calculated using B3LYP/6-311++G** and MP2/6-311++G**. The rotational free energy profiles for all of the compounds were estimated at the G3-B3 level.  相似文献   

16.
Activation barriers and reaction energetics for the three main classes of 1,3-dipolar cycloadditions, including nine different reactions, were evaluated with the MPW1K and B3LYP density functional methods, MP2, and the multicomponent CBS-QB3 method. The CBS-QB3 values were used as standards for 1,3-dipolar cycloaddition activation barriers and reaction energetics, and the density functional theory (DFT) and MP2 methods were benchmarked against these values. The MPW1K/6-31G* method and basis set performs best for activation barriers, with a mean absolute deviation (MAD) value of 1.1 kcal/mol. The B3LYP/6-31G* method and basis set performs best for reaction enthalpies, with a MAD value of 2.4 kcal/mol, while the MPW1K method shows large errors for reaction energetics. The MP2 method gives the expected systematic underestimation of barriers. Concerted and nearly synchronous transition structures are predicted by all DFT and MP2 methods. Also reported are revised estimated 0 K experimental activation enthalpies for a standard set of hydrocarbon pericyclic reactions and updated comparisons to experiment for DFT, ab initio, and multicomponent methods. B3LYP and MPW1K methods with MAD values of 1.5 and 2.1 kcal/mol, respectively, fortuitously outperform the multicomponent CBS-QB3 method, which has a MAD value of 2.3. The MAD value of the O3LYP functional improves to 2.4 kcal/mol from the previously reported 3.0 kcal/mol.  相似文献   

17.
A comprehensive exploration of the aminolysis mechanism for methyl indole-3-acetate with ammonia is carried out by employing the B3 LYP/6-311++G(d,p), M06-2 X/6-311++G(d,p) and MP2/6-311++G(d,p)//M06-2 X/6-311++G(d,p) levels. Two alterative reaction channels of the concerted and addition/elimination stepwise processes including the uncatalyzed, base-catalyzed reactions are taken into consideration. Subsequently, the substituent effects and solvent effects in methanol are also evaluated at the M06-2 X/6-311++G(d,p) level. The calculated results indicate that the calculated values of M06-2 X level are quite close to those of MP2, the stepwise pathway has more advantages to the concerted one for all of the reaction processes and the catalyst facilitates the proton migration and decreases the energy barriers as well. It is shown that the most preferred mechanism is the based-catalyzed stepwise process, the substituent of NH2 group slightly accelerates all the aminolysis reaction processes, and the solvent effect does not remarkably change the mechanism of the reaction.  相似文献   

18.
19.
Hydride‐transfer reactions between benzylic substrates and 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ) were investigated by DFT (density functional theory) calculations. The lowest unoccupied molecular orbital of DDQ has the largest extension on two carbonyl oxygens, which comes from two‐step mixing of antisymmetric orbitals of fragment π MOs. Transition‐state (TS) geometries and activation energies of reactions of four benzylic substrates R2? CH2para‐C6H4? R1 (R1, R2 = H and/or OCH3) with DDQ were calculated. M06‐2X/6‐311(+*)G* was found to be a practical computational method, giving energies and geometries similar to those of M06‐2X/6‐311++G(3df,2pd) and wB97xD/6‐311++G(3df,2pd). For toluene (R1 = R2 = H), an initiation‐propagation model was suggested, and the calculated kinetic isotope effect k(H)/k(D) = 5.0 with the tunnel correction at the propagating step is in good agreement with the experimental value 5.2. A reaction of para‐MeO? C6H4? CH2(OMe) + DDQ + (H2O)14para‐MeO? C6H4? C(?O)H + HOMe + DDQH2 + (H2O)13 was investigated by M06‐2X/6‐311(+*)G*. Four elementary processes were found and the hydride transfer (TS1) is the rate‐determining step. The hydride transfer was promoted by association with the water cluster. The size of the water cluster, (H2O)n, at TS1 was examined. Three models of n = 14, 20, and 26 were found to give similar activation energies. Metal‐free neutral hydride transfers from activated benzylic substrates to DDQ were proposed to be ready processes both kinetically and thermodynamically. © 2015 Wiley Periodicals, Inc.  相似文献   

20.
The reaction mechanisms of the 1Σ+ ground state of MS+ (M = Sc, Y, and La) with oxygen‐transfer reagent MS+ + CO → MO+ + CS in the gas phase has been proposed and investigated by ab initio methods with the 6‐31G* basis set for nonmetal atoms and the effective core potentials of Lanl2dz for the metal atoms. A carbon migration from oxygen atom to sulfur atom via a four‐center transition state is involved on the reaction potential surface. The activation energies of the reactions are 34.0, 24.1, and 36.7 kcal/mol relative to their corresponding reactants and the reaction heats are 15.7, 18.6, and 18.0 kcal/mol (respectively, for M = Sc, Y, and La) at the MP4 (SDTQ)/6‐31G*//MP2/6‐31G* level plus zero‐point energy, which indicates that the cationic yttrium sulfide is more favorable for this type of reaction. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003  相似文献   

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