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1.
A systematic study of techniques for treating noncovalent interactions within the computationally efficient density functional theory (DFT) framework is presented through comparison to benchmark-quality evaluations of binding strength compiled for molecular complexes of diverse size and nature. In particular, the efficacy of functionals deliberately crafted to encompass long-range forces, a posteriori DFT+dispersion corrections (DFT-D2 and DFT-D3), and exchange-hole dipole moment (XDM) theory is assessed against a large collection (469 energy points) of reference interaction energies at the CCSD(T) level of theory extrapolated to the estimated complete basis set limit. The established S22 [revised in J. Chem. Phys. 132, 144104 (2010)] and JSCH test sets of minimum-energy structures, as well as collections of dispersion-bound (NBC10) and hydrogen-bonded (HBC6) dissociation curves and a pairwise decomposition of a protein-ligand reaction site (HSG), comprise the chemical systems for this work. From evaluations of accuracy, consistency, and efficiency for PBE-D, BP86-D, B97-D, PBE0-D, B3LYP-D, B970-D, M05-2X, M06-2X, ωB97X-D, B2PLYP-D, XYG3, and B3LYP-XDM methodologies, it is concluded that distinct, often contrasting, groups of these elicit the best performance within the accessible double-ζ or robust triple-ζ basis set regimes and among hydrogen-bonded or dispersion-dominated complexes. For overall results, M05-2X, B97-D3, and B970-D2 yield superior values in conjunction with aug-cc-pVDZ, for a mean absolute deviation of 0.41 - 0.49 kcal/mol, and B3LYP-D3, B97-D3, ωB97X-D, and B2PLYP-D3 dominate with aug-cc-pVTZ, affording, together with XYG3/6-311+G(3df,2p), a mean absolute deviation of 0.33 - 0.38 kcal/mol.  相似文献   

2.
Acid-base thermochemistry of isolated amino acids containing oxygen or sulfur in their side chain (serine, threonine, cysteine and methionine) have been examined by quantum chemical computations. Density functional theory (DFT) was used, with B3LYP, B97-D and M06-2X functionals using the 6-31+G(d,p) basis set for geometry optimizations and the larger 6-311++G(3df,2p) basis set for energy computations. Composite methods CBS-QB3, G3B3, G4MP2 and G4 were applied to large sets of neutral, protonated and deprotonated conformers. Conformational analysis of these species, based on chemical approach and AMOEBA force field calculations, has been used to identify the lowest energy conformers and to estimate the population of conformers expected to be present at thermal equilibrium at 298 K. It is observed that G4, G4MP2, G3B3, CBS-QB3 composite methods and M06-2X DFT lead to similar conformer energies. Thermochemical parameters have been computed using either the most stable conformers or equilibrium populations of conformers. Comparison of experimental and theoretical proton affinities and Δ(acid)H shows that the G4 method provides the better agreement with deviations of less than 1.5 kJ mol(-1). From this point of view, a set of evaluated thermochemical quantities for serine, threonine, cysteine and methionine may be proposed: PA = 912, 919, 903, 938; GB = 878, 886, 870, 899; Δ(acid)H = 1393, 1391, 1396, 1411; Δ(acid)G = 1363, 1362, 1367, 1382 kJ mol(-1). This study also confirms that a non-negligible ΔpS° is associated with protonation of methionine and that the most acidic hydrogen of cysteine in the gas phase is that of the SH group. In several instances new conformers were identified thus suggesting a re-examination of several IRMPD spectra.  相似文献   

3.
Targeted therapy is currently a hot topic in the fields of cancer research and drug design. An important requirement for this approach is the development of potent and selective inhibitors for the identified target protein. However, current ways to estimate inhibitor efficacy rely on empirical protein–ligand interaction scoring functions which, suffering from their heavy parameterizations, often lead to a low accuracy. In this work, we develop a nonfitting scoring function, which consists of three terms: (1) gas‐phase protein‐ligand binding enthalpy obtained by the eXtended ONIOM hybrid method based on an integration of density functional theory (DFT) methods (XYG3 and ωB97X‐D) and the semiempirical PM6 method, (2) solvation free energy based on DFT‐SMD solvation model, and (3) entropy effect estimated by using DFT frequency analysis. The new scoring function is tested on a cyclin‐dependent kinase 2 (CDK2) inhibitor database including 76 CDK2 protein inhibitors and a p21‐activated kinase 1 (PAK1) inhibitor database including 20 organometallic PAK1 protein inhibitors. From the results, good correlations are found between the calculated scores and the experimental inhibitor efficacies with the square of correlation coefficient R2 of 0.76–0.88. This suggests a good predictive power of this scoring function. To the best of our knowledge, this is the first high level theory‐based nonfitting scoring function with such a good level of performance. This scoring function is recommended to be used in the final screening of lead structure derivatives. © 2013 Wiley Periodicals, Inc.  相似文献   

4.
Potential energy surfaces, minimum energy reaction paths, minima, transition states, reaction barriers, and conical intersections for the most important atmospheric reactions of methyl nitrate (CH(3)ONO(2)) and methylperoxy nitrite (C(3)HOONO) on the electronic ground state have been studied (i) with the second-order multiconfigurational perturbation theory (CASPT2) by computation of numerical energy gradients for stationary points and (ii) with the density functional theory (DFT). The proposed mechanism explains the conversion of unreactive alkyl peroxy radicals into alkoxy radicals: CH(3)O(2) + NO <=> CH(3)OONO <=> CH(3)O + NO(2) left arrow over right arrow CH(3)ONO(2). Additionally, several discrepancies found in the comparison of the results obtained from the two employed approaches are analyzed. CASPT2 predicts that all dissociation reactions into radicals occur without an extra exit energy barrier. In contrast, DFT finds transition states for the dissociations of cis- and trans-methylperoxy nitrite into CH(3)O + NO(2). Furthermore, multiconfigurational methods [CASPT2 and complete active space SCF (CAS-SCF)] predict the isomerization of CH3ONO2 to CH3OONO to occur in a two-step mechanism: (i) CH(3)ONO(2) --> CH(3)O + NO(2); and (ii) CH(3)O + NO(2) --> CH(3)OONO. The reason for this has to do with the coupling of the ground electronic state with the first excited state. Therefore, it is demonstrated that DFT methods based on single determinantal wave functions give an incorrect picture of the aforementioned reaction mechanisms.  相似文献   

5.
The mononuclear Mn(CO)(5)X and binuclear Mn(2)(CO)(8)(μ-X)(2) manganese carbonyl halides have long been known for the halogens Cl, Br, and I. However, the corresponding manganese carbonyl fluorides (X = F) remain unknown. The structures and thermochemistry of such manganese carbonyl fluorides and their decarbonylation products have now been investigated using density functional theory. In all cases singlet structures were found to have lower energies than the corresponding triplet structures. The expected octahedral structure is predicted for Mn(CO)(5)F. Decarbonylation of Mn(CO)(5)F is predicted to give trigonal bipyramidal Mn(CO)(4)F with equatorial fluorine. Further, decarbonylation gives tetrahedral Mn(CO)(3)F. All of the binuclear Mn(2)(CO)(n)F(2) structures (n = 8, 7, 6) are predicted to have a central Mn(2)F(2) unit with two bridging F atoms, a non-bonding Mn···Mn distance of ~3.1 ?, and exclusively terminal CO groups. The thermochemistry of these manganese carbonyl fluorides indicates that they are viable species. This suggests that the failure to date to synthesize the simple manganese carbonyl fluorides arises from a lack of a suitable synthetic method rather than from the instability of the desired products.  相似文献   

6.
Wang  Jing  Shukla  Manoj K. 《Structural chemistry》2021,32(4):1357-1363
Structural Chemistry - The degradation mechanisms of 3-nitro-1,2,4-triazol-5-one (NTO) in the bulk water were explored at the density functional theory (DFT) level using the M06-2X functional and...  相似文献   

7.
Various contemporary theoretical procedures have been tested for their accuracy in predicting the bond dissociation energies (BDEs) and the radical stabilization energies (RSEs) for a test set of 22 monosubstituted methyl radicals. The procedures considered include the high-level W1, W1', CBS-QB3, ROCBS-QB3, G3(MP2)-RAD, and G3X(MP2)-RAD methods, unrestricted and restricted versions of the double-hybrid density functional theory (DFT) procedures B2-PLYP and MPW2-PLYP, and unrestricted and restricted versions of the hybrid DFT procedures BMK and MPWB1K, as well as the unrestricted DFT procedures UM05 and UM05-2X. The high-level composite procedures show very good agreement with experiment and are used to evaluate the performance of the comparatively less expensive DFT procedures. RMPWB1K and both RBMK and UBMK give very promising results for absolute BDEs, while additionally restricted and unrestricted X2-PLYP methods and UM05-2X give excellent RSE values. UM05, UB2-PLYP, UMPW2-PLYP, UM05-2X, and UMPWB1K are among the less well performing methods for BDEs, while UMPWB1K and UM05 perform less well for RSEs. The high-level theoretical results are used to recommend alternative experimental BDEs for propyne, acetaldehyde, and acetic acid.  相似文献   

8.
Multiple mechanisms of backbiting and β‐scission reactions in free‐radical polymerization of methyl acrylate are modeled using different levels of theory, and the rigid‐rotor harmonic‐oscillator (RRHO) and hindered‐rotor (HR) approximations. We identify the most cost‐effective computational method(s) for studying the reactions and assess the effects of different factors (e.g., functional type and chain length) on thermodynamic quantities, and then identify the most likely mechanisms with first‐principles thermodynamic calculations and simulations of nuclear magnetic resonance (NMR) spectra. To this end, the composite method G4(MP2)‐6X is used to calculate the energy barrier of a representative backbiting reaction. This calculated barrier is then compared with values obtained using density functional theory (DFT) (B3LYP, M06‐2X, and PBE0) and a wavefunction‐based quantum chemistry method (MP2) to establish the benchmark method. Our study reveals that the barriers predicted using B3LYP, M06‐2X, and G4(MP2)‐6X are comparable. The entropies calculated using the RRHO and HR approximations are also comparable. DFT calculations indicate that the 1:5 backbiting mechanism with a six‐membered ring transition state and 1:7 backbiting with an eight‐membered ring transition state are energetically more favored than 1:3 backbiting and 1:9 backbiting mechanisms. The thermodynamic favorability of 1:5 versus 1:7 backbiting depends on the live polymer chain length. The activation energies and rate constants of the left and right β‐scission reactions are nearly equal. The calculated and experimental 13C and 1H NMR chemical shifts of polymer chains affected by backbiting and β‐scission reactions agree with each other, which provides further evidence in favor of the proposed mechanisms. © 2013 Wiley Periodicals, Inc.  相似文献   

9.
The effects of aqueous solvation on the thermochemistry of reactions between mercury and small halogen molecules has been investigated by the microsolvation approach using ab initio and density functional theory (DFT) calculations. The structures, vibrational frequencies, and binding energies of 1, 2, and 3 water molecules with mercury-halide (HgBr2, HgBrCl, HgCl2, HgBr, and HgCl) and related mercury and halogen species (Br2, BrCl, Cl2, Cl, Hg, and Br) have been computed with second order M?ller-Plesset perturbation theory (MP2) and the B3LYP density functional method. Accurate incremental water binding energies have been obtained at the complete basis set (CBS) limit using sequences of correlation consistent basis sets, including higher order correlation effects estimated from coupled cluster calculations. The resulting energetics were used to calculate the influence of water molecules on the thermochemistry of a number of reactions between mercury and small halogen-containing molecules. In general, the presence of water favors the formation of oxidized mercury halide species.  相似文献   

10.
使用了不同密度泛函方法计算X-H (X = C, N, O, Si, P, S) 键离解能,并分析不同密度泛函方法的计算精度。研究发现大多数密度泛函方法包括B3LYP, B3P86, B3PW91, G96LYP, PBE1PBE,和BH&HLYP都明显低估键离解能13-25 kJ/mol。该现象与是否使用无限基组无关,因为即使使用无限基组键离解能仍然被低估。因此密度泛函方法不适合用于键离解能的估算。其中B3P86方法的偏差最小。进一步分析表明,使用限制性开壳层计算并无任何优势,在大多数情况下非限制性开壳层计算实际上比限制性开壳层计算要好。最后,我们发现了密度泛函方法对键离解能的低估是系统的,因此建议利用校准后的UDFT/6-311++G(d, p)方法计算化学键离解能。  相似文献   

11.
Detailed knowledge of hydrocarbon radical thermochemistry is critical for understanding diverse chemical phenomena, ranging from combustion processes to organic reaction mechanisms. Unfortunately, experimental thermochemical data for many radical species tend to have large errors or are lacking entirely. Here we develop procedures for deriving high-quality thermochemical data for hydrocarbon radicals by extending Wheeler et al.'s "generalized bond separation reaction" (GBSR) scheme (J. Am. Chem. Soc., 2009, 131, 2547). Moreover, we show that the existing definition of hyperhomodesmotic reactions is flawed. This is because transformation reactions, in which one molecule each from the predefined sets of products and reactants can be converted to a different product and reactant molecule, are currently allowed. This problem is corrected via a refined definition of hyperhomodesmotic reactions in which there are equal numbers of carbon-carbon bond types inclusive of carbon hybridization and number of hydrogens attached. Ab initio and density functional theory (DFT) computations using the expanded GBSRs are applied to a newly derived test set of 27 hydrocarbon radicals (HCR27). Greatly reduced errors in computed reaction enthalpies are seen for hyperhomodesmotic and other highly balanced reactions classes, which benefit from increased matching of hybridization and bonding requirements. The best performing DFT methods for hyperhomodesmotic reactions, M06-2X and B97-dDsC, give average deviations from benchmark computations of only 0.31 and 0.44 (±0.90 and ±1.56 at the 95% confidence level) kcal/mol, respectively, over the test set. By exploiting the high degree of error cancellation provided by hyperhomodesmotic reactions, accurate thermochemical data for hydrocarbon radicals (e.g., enthalpies of formation) can be computed using relatively inexpensive computational methods.  相似文献   

12.
We present density functional theory (DFT) interaction energies for the sandwich and T‐shaped conformers of substituted benzene dimers. The DFT functionals studied include TPSS, HCTH407, B3LYP, and X3LYP. We also include Hartree–Fock (HF) and second‐order Møller–Plesset perturbation theory calculations (MP2), as well as calculations using a new functional, P3LYP, which includes PBE and HF exchange and LYP correlation. Although DFT methods do not explicitly account for the dispersion interactions important in the benzene–dimer interactions, we find that our new method, P3LYP, as well as HCTH407 and TPSS, match MP2 and CCSD(T) calculations much better than the hybrid methods B3LYP and X3LYP methods do. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006  相似文献   

13.
The reaction enthalpy (298 K), barrier (0 K), and activation energy and preexponential factor (600-800 K) have been examined computationally for the abstraction of hydrogen from benzene by the methyl radical, to assess their sensitivity to the applied level of theory. The computational methods considered include high-level composite procedures, including W1, G3-RAD, G3(MP2)-RAD, and CBS-QB3, as well as conventional ab initio and density functional theory (DFT) methods, with the latter two classes employing the 6-31G(d), 6-31+G(d,p) and/or 6-311+G(3df,2p) basis sets, and including ZPVE/thermal corrections obtained from 6-31G(d) or 6-31+G(d,p) calculations. Virtually all the theoretical procedures except UMP2 are found to give geometries that are suitable for subsequent calculation of the reaction enthalpy and barrier. For the reaction enthalpy, W1, G3-RAD, and URCCSD(T) give best agreement with experiment, while the large-basis-set DFT procedures slightly underestimate the endothermicity. The reaction barrier is slightly more sensitive to the choice of basis set and/or correlation level, with URCCSD(T) and the low-cost BMK method providing values in close agreement with the benchmark G3-RAD value. Inspection of the theoretically calculated rate parameters reveals a minor dependence on the level of theory for the preexponential factor. There is more sensitivity for the activation energy, with a reasonable agreement with experiment being obtained for the G3 methods and the hybrid functionals BMK, BB1K, and MPW1K, especially in combination with the 6-311+G(3df,2p) basis set. Overall, the high-level G3-RAD composite procedure, URCCSD(T), and the cost-effective DFT methods BMK, BB1K, and MPW1K give the best results among the methods assessed for calculating the thermochemistry and kinetics of hydrogen abstraction by the methyl radical from benzene.  相似文献   

14.
Hydrogen/deuterium exchange reactions involving protonated triglycine and deuterated ammonia (ND(3)) have been examined in the gas phase using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Ab initio and density functional theory (DFT) calculations have been carried out to model the exchanges and to obtain energetics and vibrational frequencies for molecules involved in the proposed exchange mechanisms. Structural optimization and frequency calculations have been performed at the B3LYP level of theory with the 6-311+G(d,p) basis set. Transition states have been calculated at the same level of theory and basis set as above using the QST2 and QST3 methods. Single-point energy calculations have been performed at the MP2/6-311+G(d,p) level. Six labile sites of protonated triglycine were found to undergo H/D exchange. Of these six labile hydrogens, two are amide, three are ammonium, and one is carboxyl. Detailed mechanisms for each of these transfers are proposed. Qualitative onium ion and tautomer mechanisms for the exchanges of ammonium and amide hydrogens, respectively, using semiempirical calculations were suggested in previous studies by Beauchamp et al. As shown by the current ab initio and DFT calculations completed during this study, the mechanisms proposed in that study are notionally correct; however, the tautomer mechanisms are shown here to be the result of the fact that a second stable isomer of protonated triglycine exists in which the amide1 carbonyl oxygen is protonated. The exchange of the carboxyl hydrogen is found to proceed via a transition state resembling an ammonium ion interacting with a carboxylate moiety via two hydrogen bonds. The current work thus provides significant mechanistic and structural detail for a considerably more in-depth understanding of the processes involved in gas phase H/D exchange of peptides.  相似文献   

15.
In this work, we examine the performance of XYG3, a newly developed doubly hybrid density functional (Zhang, Xu, and Goddard III, Proc Natl Acad Sci USA 2009, 106, 4963), to calculate covalent bond dissociation enthalpy (BDE). We use 5 atoms, 32 molecular radicals, and 116 closed-shell molecules to set up 142 bond dissociation reactions. For the total of 148 heats of formation (HOFs) and 142 BDEs, XYG3 leads to mean absolute deviations (MADs) of 1.45 and 1.87 kcal/mol, respectively. In comparison with some other functionals, MADs for HOFs are 2.31 (M06-2X), 2.98 (B2PLYP-D), 3.04 (BMK), 3.96 (B3LYP), 4.47 (B2PLYP), 5.42 (B2GP-PLYP), 6.46 (PBE0), and 29.93 kcal/mol (B3P86), and the corresponding errors for BDEs are 2.06 (M06-2X), 2.25 (BMK), 2.51 (B2PLYP-D), 2.89 (B2GP-PLYP), 3.30 (B3P86), 3.44 (B2PLYP), 3.87 (PBE0), and 6.14 kcal/mol (B3LYP).  相似文献   

16.
We are proposing a new computational thermochemistry protocol denoted W3 theory, as a successor to W1 and W2 theory proposed earlier [Martin and De Oliveira, J. Chem. Phys. 111, 1843 (1999)]. The new method is both more accurate overall (error statistics for total atomization energies approximately cut in half) and more robust (particularly towards systems exhibiting significant nondynamical correlation) than W2 theory. The cardinal improvement rests in an approximate account for post-CCSD(T) correlation effects. Iterative T3 (connected triple excitations) effects exhibit a basis set convergence behavior similar to the T3 contribution overall. They almost universally decrease molecular binding energies. Their inclusion in isolation yields less accurate results than CCSD(T) nearly across the board: It is only when T4 (connected quadruple excitations) effects are included that superior performance is achieved. T4 effects systematically increase molecular binding energies. Their basis set convergence is quite rapid, and even CCSDTQ/cc-pVDZ scaled by an empirical factor of 1.2532 will yield a quite passable quadruples contribution. The effect of still higher-order excitations was gauged for a subset of molecules (notably the eight-valence electron systems): T5 (connected quintuple excitations) contributions reach 0.3 kcal/mol for the pathologically multireference X 1Sigmag+ state of C2 but are quite small for other systems. A variety of avenues for achieving accuracy beyond that of W3 theory were explored, to no significant avail. W3 thus appears to represent a good compromise between accuracy and computational cost for those seeking a robust method for computational thermochemistry in the kJ/mol accuracy range on small systems.  相似文献   

17.
18.
We present a number of near-exact, nonrelativistic, Born-Oppenheimer reference data sets for the parametrization of more approximate methods (such as DFT functionals). The data were obtained by means of the W4 ab initio computational thermochemistry protocol, which has a 95% confidence interval well below 1 kJ/mol. Our data sets include W4-08, which are total atomization energies of over 100 small molecules that cover varying degrees of nondynamical correlations, and DBH24-W4, which are W4 theory values for Truhlar's set of 24 representative barrier heights. The usual procedure of comparing calculated DFT values with experimental atomization energies is hampered by comparatively large experimental uncertainties in many experimental values and compounds errors due to deficiencies in the DFT functional with those resulting from neglect of relativity and finite nuclear mass. Comparison with accurate, explicitly nonrelativistic, ab initio data avoids these issues. We then proceed to explore the performance of B2x-PLYP-type double hybrid functionals for atomization energies and barrier heights. We find that the optimum hybrids for hydrogen-transfer reactions, heavy-atoms transfers, nucleophilic substitutions, and unimolecular and recombination reactions are quite different from one another: out of these subsets, the heavy-atom transfer reactions are by far the most sensitive to the percentages of Hartree-Fock-type exchange y and MP2-type correlation x in an (x, y) double hybrid. The (42,72) hybrid B2K-PLYP, as reported in a preliminary communication, represents the best compromise between thermochemistry and hydrogen-transfer barriers, while also yielding excellent performance for nucleophilic substitutions. By optimizing for best overall performance on both thermochemistry and the DBH24-W4 data set, however, we find a new (36,65) hybrid which we term B2GP-PLYP. At a slight expense in performance for hydrogen-transfer barrier heights and nucleophilic substitutions, we obtain substantially better performance for the other reaction types. Although both B2K-PLYP and B2GP-PLYP are capable of 2 kcal/mol quality thermochemistry, B2GP-PLYP appears to be the more robust toward nondynamical correlation and strongly polar character. We additionally find that double-hybrid functionals display excellent performance for such problems as hydrogen bonding, prototype late transition metal reactions, pericyclic reactions, prototype cumulene-polyacetylene system, and weak interactions.  相似文献   

19.
The potential energy surface (PES) for the H + CH4 system has been constructed with the recently developed XYG3 doubly hybrid functional, while those with the standard B3LYP hybrid functional, and the Møller–Plesset perturbation theory up to the second order (MP2) are also presented for comparison. Quantum dynamics studies demonstrated that satisfactory results on the reaction probabilities and the rate coefficients can be obtained on top of the XYG3‐PES, as compared to the results based on the highly accurate, yet expensive, CCSD(T)‐PES (Li et al., J. Chem. Phys. 2015, 142, 204302). Further investigation suggested that the XYG3 functional is useful in providing accurate rate coefficients for some larger systems involving H atom abstractions. © 2017 Wiley Periodicals, Inc.  相似文献   

20.
Density functional theory (DFT) studies were performed to investigate the influence of coadsorbates on the nitrogen oxide dissociation on the vicinal rhodium(311) surface. This study amplifies prior studies on the dissociation of oxygen and nitrogen oxide on the (111) facet of rhodium. The influence of coadsorbates on the kinetic parameters and thermochemistry of the NO dissociation on Rh311 was studied. In addition, the activation energy and thermochemistry of this reaction were determined as a function of oxygen preoccupation/initial coverage. Steric and electronic effects and their influence on the dissociation reaction were examined. The results are discussed in the face of an NOx dissociation catalyst system proposed by Nakatsuji.  相似文献   

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