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1.
The temperature dependent field ionization mass spectrometry method combined with ab initio calculations was used to determine the interaction energies and the structures of 9-methylguanine-acrylamide dimers. Acrylamide mimics the side chain amide group of the natural amino acids asparagine and glutamine. The experimental enthalpy of the dimer formation derived from the van't Hoff plot is ?59.5 ± 3.8 kJ mol?1. The value is higher than interaction energies between acrylamide and other nucleic acid bases which were determined to be ?57.0 for 1-methylcytosine, ?52.0 for 9-methyladenine, and ?40.6 kJ mol?1 for 1-methyl-uracil. In total, eight hydrogen bonded dimers formed by the three lowest energy 9-methylguanine tautomers and acrylamide were found in the quantum chemical calculations performed at the DFT/B3LYP/6-31++G?? and MP2/6-31++G?? levels of theory. The relative stability and the interaction energies of the dimers were calculated accounting for the basis set superposition error and the zero-point vibrational energy correction. The lowest energy dimer found in the calculations is formed by acrylamide (Ac) with the keto tautomer of 9-methylguanine (Gk). It is stabilized by two intermolecular H bonds, C6=O(Gk) · · · H—N(Ac) and Nl—H(Gk) · · ·O(Ac), and it is more stable than the second lowest energy dimer by ≈ 25 kJ mol?1. The calculated interaction energies of the lowest energy 9-methylguanine-acrylamide dimer are ?65.0 kJ mol?1 and ?67.7 kJ mol?1 at the MP2 and DFT levels of theory, respectively. The experimental enthalpy of the dimer formation is in good agreement with both the calculated interaction energies of the GkAc dimer and much higher than the interaction energies calculated for all other 9-methylguanine-acrylamide dimers. This proved that only one dimer was present in the experimental samples. To verify whether acrylamide is a good model of the amino acid-amide group, we performed direct calculations of the 9-methylguanine-glutamine dimers at the same levels of theory as used for the complexes involving acrylamide. The interaction energies found for the lowest energy 9-methylguanine-glutamine dimer are ?65.1 kJ mon?1 (MP2/6-31++G??) and ?66.2 kJ mol?1 (DFT/B3LYP/6-31++G??) and these values are very close (within 0.5 kJ mol?1) to the interaction energies obtained for the 9-methylguanine-acrylamide dimers.  相似文献   

2.
It is shown that the closed shell valence electron molecular correlation energy of organic molecules in their ground states is a homogeneous multilinear function of the numbers of neutral atoms in their canonical hybridization state. The additivity is a robust feature, which holds for MP2(fc), MP3(fc) and MP4(fc) model calculations. The latter results obtained on a test set of 91 widely different organic molecules, exhibiting a whole gamut of electronic structure patterns, are excellent as evidenced by the absolute average deviation from the additivity values (AAD) of only 1.4 kcal mol?1 and R 2 = 0.999 93. The maximum absolute deviation (MAD) is 5.3 kcal mol?1. The additivity formula for the total molecular electron correlation retrieved from G3 calculations also has an excellent performance (AAD = 1.2 kcal mol?1, R 2 = 0.999 98 and MAD = 7.2 kcal mol?1). If it is taken into account that the additivity formulae require only back of the envelope calculations, these results are remarkable indeed, in particular since the G3 correlation energies span a very large range from 180.7 (methane) to 1642.8 (hexafluorocyclopropane) kcal mol?1. Comparison of the exact electron correlation energies in free atoms with the corresponding average correlation energies in molecules reveals that a substantial increase in the latter provides an important contribution in overcoming a very strong Coulomb repulsion between the nuclei. It is shown that the additivity formulae are useful in detecting some special molecular features such as strong resonance and anti-aromaticity.  相似文献   

3.
The interaction within the methane–methane (CH4/CH4), perfluoromethane–perfluoromethane (CF4/CF4) methane–perfluoromethane dimers (CH4/CF4) was calculated using the Hartree–Fock (HF) method, multiple orders of Møller–Plesset perturbation theory [MP2, MP3, MP4(DQ), MP4(SDQ), MP4(SDTQ)], and coupled cluster theory [CCSD, CCSD(T)], as well as the PW91, B97D, and M06-2X density functional theory (DFT) functionals. The basis sets of Dunning and coworkers (aug-cc-pVxZ, x?=?D, T, Q), Krishnan and coworkers [6-311++G(d,p), 6-311++G(2d,2p)], and Tsuzuki and coworkers [aug(df, pd)-6-311G(d,p)] were used. Basis set superposition error (BSSE) was corrected via the counterpoise method in all cases. Interaction energies obtained with the MP2 method do not fit with the experimental finding that the methane–perfluoromethane system phase separates at 94.5?K. It was not until the CCSD(T) method was considered that the interaction energy of the methane–perfluoromethane dimer (?0.69?kcal?mol?1) was found to be intermediate between the methane (?0.51?kcal?mol?1) and perfluoromethane (?0.78?kcal?mol?1) dimers. This suggests that a perfluoromethane molecule interacts preferentially with another perfluoromethane (by about 0.09?kcal?mol?1) than with a methane molecule. At temperatures much lower than the CH4/CF4 critical solution temperature of 94.5?K, this energy difference becomes significant and leads perfluoromethane molecules to associate with themselves, forming a phase separation. The DFT functionals yielded erratic results for the three dimers. Further development of DFT is needed in order to model dispersion interactions in hydrocarbon/perfluorocarbon systems.  相似文献   

4.
Local models for the triples part of the MP4 or CCSD(T) energy are formulated in terms of atom-labelled functions to describe the occupied and virtual orbital spaces. These models retain triple substitutions in which at most one of the three orbital replacements involves a change of atom. This reduces the number of triple substitutions from scaling with the 6th power of molecule size to scaling with the 4th power, and reduces the computational cost from 7th order to 5th order. Non-locality in the triple substitutions is dominated by terms in which an electron is scattered twice, while the other two singly scattered electrons exhibit non-locality that is similar to that seen in double substitutions. Two non-iterative computational models are designed around this observation. The first, ionic2, allows for non-locality only in the doubly-scattered electron, and recovers around 95% of the triples correlation energy (in the large-molecule limit). The second, ionic*, also approximately accounts for the effect of simultaneous non-locality of the doubly-scattered electron and the singly scattered electrons, and recovers over 99% of the triples energy. The latter yields a maximum error of 0.23?kcal?mol?1 and an RMS error of 0.05?kcal?mol?1 in the MP4/6-31G* triples energies of 179 closed shell molecules from the G3 database. A one-parameter empirical local model is introduced which recovers typically 99.7% of the MP4 triples correlation energy, and reduces the maximum error to 0.03?kcal?mol?1 and the RMS error to 0.01?kcal?mol?1. An implementation of these models is described which manifests the 5th-order scaling of cost with molecule size, without requiring storage of the local triples or the vvvo integrals.  相似文献   

5.
6.
The low-energy region of the intermolecular potential energy hypersurface (PES) of the ammonia dimer was studied at the level of second-order Moller-Plesset perturbation theory (MP2) using a very large basis set. Individual minima were located on the PES employing the counterpoise (CP) correction to account for the basis set superposition error (BSSE). Apart from these canonical MP2 calculations local MP2 (LMP2) calculations were performed. For the latter the BSSE at the correlated level is inherently absent by virtue of the local truncation of the virtual space. Results from canonical and local MP2 calculations are compared and the reliability of the LMP2 method for intermolecular complexes and clusters is discussed. The canonical MP2 calculations predicted five minimum structures, the four most stable ones lying energetically very close. For these four structures single point MP2 energy calculations with a further extended basis set (1024 functions for the ammonia dimer) were performed. The equilibrium dissociation energies so obtained are close to the one-particle basis set limit, as illustrated by a remaining BSSE of less than 0.2 kJ mol?1. The geometry optimizations at the LMP2 level, using the three most stable canonical MP2 structures as initial geometries, all collapsed to a single minimum corresponding to an asymmetric structural arrangement. A canonical MP2 single point calculation, at that geometry, revealed that the LMP2 minimum structure is virtually as stable as the lowest minima on the canonical MP2 PES. Based on these calculations the global minimum of the ammonia dimer was assigned to a part of the PES represented by an asymmetric structure with an equilibrium dissociation energy of 13.5±0.3 kJ mol?1  相似文献   

7.
Presuming zeroth-order electronic wavefunctions generated from localized SCF or FORS molecular orbitals, the correlation energy is expressed as a bilinear form in terms of the pair populations of these orbitals and the projections of a correlation operator onto these orbitals. The latter are determined by fitting the correlation energies of large sets of organic molecules, which are reproduced with a mean absolute deviation of 1–3 kcal mol?1. The resulting formula provides a ‘back-of-the-envelope’ method for estimating correlation energies and furnishes an analysis of these energies in terms of physical concepts and chemical structure. It Predicts the correlation energy of diamond (per carbon atom) to within 6 kcal mol?1.  相似文献   

8.
《Molecular physics》2012,110(19-20):2477-2491
Accurate isomerization energies are obtained for a set of 45 C8H8 isomers by means of the high-level, ab initio W1-F12 thermochemical protocol. The 45 isomers involve a range of hydrocarbon functional groups, including (linear and cyclic) polyacetylene, polyyne, and cumulene moieties, as well as aromatic, anti-aromatic, and highly-strained rings. Performance of a variety of DFT functionals for the isomerization energies is evaluated. This proves to be a challenging test: only six of the 56 tested functionals attain root mean square deviations (RMSDs) below 3?kcal?mol?1 (the performance of MP2), namely: 2.9 (B972-D), 2.8 (PW6B95), 2.7 (B3PW91-D), 2.2 (PWPB95-D3), 2.1 (ωB97X-D), and 1.2 (DSD-PBEP86) kcal?mol?1. Isomers involving highly-strained fused rings or long cumulenic chains provide a ‘torture test’ for most functionals. Finally, we evaluate the performance of composite procedures (e.g. G4, G4(MP2), CBS-QB3, and CBS-APNO), as well as that of standard ab initio procedures (e.g. MP2, SCS-MP2, MP4, CCSD, and SCS-CCSD). Both connected triples and post-MP4 singles and doubles are important for accurate results. SCS-MP2 actually outperforms MP4(SDQ) for this problem, while SCS-MP3 yields similar performance as CCSD and slightly bests MP4. All the tested empirical composite procedures show excellent performance with RMSDs below 1?kcal?mol?1.  相似文献   

9.
The aim of the present study was to perform a quantum chemical investigation in the 1,2-hydrogen shift reaction for the PH2X and HPX molecules (X = F,Cl). Several phosphorus–halogen-bearing molecules were studied, including PH2F, PH2Cl, HPF, HPCl, HPFH, HPClH, PFH and PClH. The energies of stationary and saddle points on the ground electronic potential energy surface were investigated with post-Hartree–Fock methods [CCSD(T), MP2, QCISD] and different DFT functionals. The PH2F 1,2-hydrogen shift energy barrier was 75 kcal mol?1 at the CCSD(T) level and only a small increase in this value was observed for the HPF isomerisation. In contrast, the HPCl 1,2-hydrogen shift barrier is higher than the PH2Cl one, which presented a barrier height of 69 kcal mol?1 among CCSD(T) and composite methods. The rate constants of these unimolecular rearrangements varied from 10?44 to 10?38 s?1, and these isomerisation channels exhibited large half-lives. In addition, the heat of formation of each monohalogenophosphane was also calculated. The Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) analysis were also employed to characterise the differences between the phosphorous–halogen bonds.  相似文献   

10.
CCSD(T) and MP2 results using the aug-cc-pV5Z basis set are reported for chain, cyclic and other structures of the clusters (H2)n, n?=?2-8, (CO2)n, n?=?2-6 and (HF)n, n?=?2-8. In chain-like structures of (H2)n and (CO2)n, with the bonding type of the dimer maintained, the dissociation energy De of the dimer doubles for the trimer, triples for the tetramer, and so on. Due to these systems being dominated by short-range forces, interactions are essentially restricted to neighbouring monomers. For other types of (H2)n and (CO2)n structures, the multipliers relative to the dimerisation energy can be much higher. Dissociation energies for the hexamers in S6 symmetry of both H2 (379?cm?1) and CO2 (4925?cm?1) are over ten times the respective dimerisation energies. For the chain-like trimer of HF, however, De is in excess of double the dimer value. Mainly due to longer-range dipolar forces, the interactions reach beyond the neighbouring monomers. The interaction energy between HF monomers in chains follows an approximate R?2 (R being the F–F distance) relationship, The calculated dissociation energies of the HF octamer are 15,985?cm?1 (factor of 10.4) for the chain, and 21,003?cm?1 (factor of 13.7) for the C6h cyclic structure.  相似文献   

11.
High-level ab initio electronic structure calculations up to the CCSD(T) theory level, including extrapolations to the complete basis set (CBS) limit, resulted in high precision energetics of the tautomeric equilibrium in 2-substituted acetaldehydes (XH2C-CHO). The CCSD(T)/CBS relative energies of the tautomers were estimated using CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z calculations with MP2/aug-cc-pVTZ geometries. The relative enol (XHC?=?CHOH) stabilities (ΔE e,CCSD(T)/CBS) were found to be 5.98?±?0.17, ?1.67?±?0.82, 7.64?±?0.21, 8.39?±?0.31, 2.82?±?0.52, 10.27?±?0.39, 9.12?±?0.18, 5.47?±?0.53, 7.50?±?0.43, 10.12?±?0.51, 8.49?±?0.33, and 6.19?±?0.18?kcal?mol?1 for X?=?BeH, BH2, CH3, Cl, CN, F, H, NC, NH2, OCH3, OH, and SH, respectively. Inconsistencies between the results of complex/composite energy computations methods Gn/CBS (G2, G3, CBS-4M, and CBS-QB3) and high-level ab initio methods (CCSD(T)/CBS and MP2/CBS) were found. DFT/aug-cc-pVTZ results with B3LYP, PBE0 (PBE1PBE), TPSS, and BMK density functionals were close to the CCSD(T)/CBS levels (MAD?=?1.04?kcal?mol?1).  相似文献   

12.
Abstract

To understand and model the solvation of the hydroxide ion, OH(H2O)? n clusters, n = 1?5, are studied using ab initio quantum chemical techniques, largely at the MP2 level of theory using a double zeta plus polarization functions basis extended by diffuse functions. Energies and vibrational frequencies, together with thermodynamic quantities such as enthalpies, entropies and Gibbs free energies, are computed. This permits comparison with experimental estimates of the successive thermodynamic changes associated with the reaction OH(H2O)? n + H2O → OH(H2O)? n+1. The theoretical values are in good agreement with experiment. The free energy of hydration of OH? is modelled by a composite discrete-continuum method where the effects of the first hydration shell (n = 3) are obtained from the gas phase cluster calculation, while the long-range effects are modelled using self consistent reaction field theory, namely by calculating the solvation energy of OH(H2O)? n in a dielectric continuum. The best estimate of the solvation (free) energy at 298 K is ?84·5 kcal mol?1, compared to the experimental value of ?102·8 kcal mol?1.  相似文献   

13.
Cleavage of disulfide bonds is a common method used in linking peptides to proteins in biochemical reactions. The structures, internal rotor potentials, bond energies, and thermochemical properties (ΔfH°, S°, and Cp(T)) of the S–S bridge molecules CH3SSOH and CH3SS(=O)H and the radicals CH3SS?=O and C?H2SSOH that correspond to H‐atom loss are determined by computational chemistry. Structure and thermochemical parameters (S° and Cp(T)) are determined using density functional Becke, three‐parameter, Lee–Yang–Parr (B3LYP)/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p). The enthalpies of formation for stable species are calculated using the total energies at B3LYP/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p), and the higher level composite CBS–QB3 levels with work reactions that are close to isodesmic in most cases. The enthalpies of formation for CH3SSOH, CH3SS(=O)H are ?38.3 and ?16.6 kcal mol?1, respectively, where the difference is in enthalpy RSO–H versus RS(=O)–H bonding. The C–H bond energy of CH3SSOH is 99.2 kcal mol?1, and the O–H bond energy is weaker at 76.9 kcal mol?1. Cleavage of the weak O–H bond in CH3SSOH results in an electron rearrangement upon loss of the CH3SSO–H hydrogen atom; the radical rearranges to form the more stable CH3SS· = O radical structure. Cleavage of the C–H bond in CH3SS(=O)H results in an unstable [CH2SS(=O)H]* intermediate, which decomposes exothermically to lower energy CH2 = S + HSO. The CH3SS(=O)–H bond energy is quite weak at 54.8 kcal mol?1 with the H–C bond estimated at between 91 and 98 kcal mol?1. Disulfide bond energies for CH3S–SOH and CH3S–S(=O)H are low: 67.1 and 39.2 kcal mol?1. Copyright © 2011 John Wiley & Sons, Ltd.  相似文献   

14.
Abstract

In acetonitrile solutions, the exchange reaction is bimolecular in the Tl+ + 18C6 system, while in the Tl+ + pentaglyme system the associative-dissociative and the bimolecular mechanisms coexist at room temperature and the bimolecular exchange reaction dominates at 263° K. For the bimolecular mechanism in the case of Tl+ + 18C6 and the associative-dissociative mechanism in the case of Tl+ + pentaglyme, the activation energies of the exchange reactions change with temperature. At 298° K, in the Tl+ + 18C6 system the activation energy for the bimolecular exchange reaction is ≈ 2 kcal.mol?1 and exchange rate constant (k1) is (4.1 ± 0.1) × 107 s?1mol?1; in the Tl+ + pentaglyme system, the activation energy for the associative-dissociative exchange reaction is ≈ 5 kcal mol?1 and the decomplexation rate constant (k?2) is (2.2 ± 0.4) X 105 s?1. The activation energy for the bimolecular exchange in the Tl+ + pentaglyme system was determined to be 3.00 ± 0.05 kcal.mol?1 and the exchange rate constant (3.0 ± 0.1) X 108 s?1 mol?1.  相似文献   

15.
A study of the regioselectivity of protonation of captodative trifluoromethylated enamines was carried out using MP2/6‐311 + G(d,p) calculations and the natural bond orbital analysis. The central issue of this research concerns the influence of the electron‐withdrawing group, which is not capable of the π,π‐conjugation, on the properties of captodative enamines and their salts. The presence of CF3 group in such type of enamines levels the energy of their N‐protonated and C‐protonated forms. The transition states were found for both intramolecular and intermolecular processes of the proton transfer. The more possible mechanism of the isomerization of enammonium and iminium cations includes the proton transfer from N‐protonated form to olefinic carbon atom of the starting enamine. The transition state energies, which correspond to intermolecular process, are relatively low (11–13 kcal mol–1) in contrast to the intramolecular pathway (64–69 kcal mol–1). Copyright © 2011 John Wiley & Sons, Ltd.  相似文献   

16.
Raman spectra of HiPco SWNT and SWNT-pyrene films were measured in the 160–1800 cm?1 range. Due to the non-covalent interaction between SWNT and pyrene the most intensive component of the SWNT G mode (1590 cm?1) is downshifted by 2 cm?1 and becomes narrower. Also the intensity of the low-frequency component of the G mode (1550 cm?1) decreases by about 30%. Structures and interaction energies in the complexes of pyrene and zigzag (n, 0) SWNTs [6 ≤ n ≤ 20] were determined at the MP2 level of theory. The BSSE-free geometry optimization of the pyrene-zigzag (12,0) SWNT complex converged to a structure with a 1/2staggered conformation and with an intermolecular distance of 3.5 Å. The BSSE-free interaction energy in the complex is ?30.8 kj mol?1. Increasing of the nanotube diameter leads to a higher interaction energy. This energy becomes equal to ?37.2 kJ mol?1 in the case of a planar carbon surface.  相似文献   

17.
From large basis set coupled cluster calculations and a minor empirical adjustment, an anharmonic force field for silane has been derived that is consistently of spectroscopic quality (±1 cm?1 on vibrational fundamentals) for all isotopomers of silane studied. Inner-shell polarization functions have an appreciable effect on computed properties and even on anharmonic corrections. From large basis set coupled cluster calculations and extrapolations to the infinite-basis set limit, we obtain TAE0 = 303.80 ± 0.18 kcal mol?1, which includes an anharmonic zero-point energy (19.59 kcal mol?1), inner-shell correlation (—0.36 kcal mol?1), scalar relativistic corrections (— 0.70 kcal mol?1) and atomic spin-orbit corrections (—0.43 kcal mol?1). In combination with the recently revised ΔH o f, o[Si(g)], we obtain ΔH o f.o[SiH4(g)] = 9.9 ± 0.4 kcal mol?1 in between the two established experimental values.  相似文献   

18.
We report the observation of extensive a- and c-type rotation-tunnelling (RT) spectra of (H2O)2 for Ka = 0–3, and (D2O)2 for Ka = 0–4. These data allow a detailed characterization of the vibrational ground state to energies comparable to those of the low-lying (70–80 cm?1) intermolecular vibrations. We present a comparison of the experimentally determined molecular constants and tunnelling splittings with those calculated on the VRT(ASP-W)III, SAPT-5st, and VRT(MCY-5f) intermolecular potential energy surfaces. The SAPT-5st potential reproduces the vibrational ground state properties of the water dimer very well. The VRT(MCY-5f) and especially the VRT(ASP-W)III potentials show larger disagreements, in particular for the bifurcation tunnelling splitting.  相似文献   

19.
Ab initio energy band structure calculations of infinite single and double HF chains are performed. Interaction energies within and between the linear macromolecules are deduced. As an alternative way for the decomposition of the binding energy tetrameric HF clusters are investigated. Second order perturbation theory is applied to calculate the correlation energy contributions. The interaction of the elementary cell with its neighboring cells in the same layer is repulsive. A binding energy is obtained for the interaction with cells in different layers. The cohesive energy is about - 2 kcal mol-1 with respect to a single HF dimer. The results show that the binding energy in molecular crystals can be determined with the help of molecular cluster calculations.  相似文献   

20.
The heats of formation of haloacetylenes are evaluated using the recent W1 and W2 ab initio computational thermochemistry methods. These calculations involve CCSD and CCSD(T) coupled cluster methods, basis sets of up to spdfgh quality, extrapolations to the one-particle basis set limit, and contributions of inner-shell correlation, scalar relativistic effects. and (where relevant) first-order spin-orbit coupling. The heats of formation determined using W2 theory are: δH1 298(HCCH) = 54.48 kcal mol?1, δHf 298(HCCH) = 25.15 kcal mol, δHf 298(FCCF) = 1.38 kcal mol?1, δHf 298(HCCC1) = 54.83 kcal mol?1, δHf 298(CICCC1) = 56.21 kcal mol?1, and δHf 298(FCCC1) = 28.47 kcal mo1?1. Enthalpies of hydrogenation and destabilization energies relative to acetylene were obtained at the WI level of theory. So doing we find the following destabilization order for acetylenes: FCCF > ClCCF > HCCF > ClCCCl > HCCCI > HCCH. By a combination of WI theory and isodesmic reactions. we show that the generally accepted heat of formation of 1,2-dichloroethane should be revised to ?31.8 ± 0.6 kcal mol?1, in excellent agreement with a very recent critically evaluated review. The performance of compound thermochemistry schemes, such as G2, G3, G3X and CBS-QB3 theories, has been analysed.  相似文献   

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