Accurate ab initio calculation of the Ar–CF4 intermolecular potential energy surface

Ar–CF₄ intermolecular interaction potential is studied by ab initio calculations at the MP2 and CCSD(T) levels of theory containing the so-called bond functions ({3s3p2d1f} basis set was chosen) both with and without a correction for the basis-set superposition error. The calculations were performed with Dunning's correlation consistent basis sets (aug-cc-pVXZ, X = D, T, Q, 5) to extrapolate the Ar–CF₄ potential energy minimum and intermolecular distance to their complete basis set (CBS) limits. It is shown that the addition of bond functions results in a dramatic improvement in the convergence of the calculated interaction energies at the MP2/aug-cc-pVTZ level. The MP2/{3s3p2d1f}-aug-cc-pVTZ potential energy surface even approaches the CCSD(T)/aug-cc-pVQZ potential energy surface. The potential energy minima and the intermolecular distances are both significantly closer to the CBS limit when using the bond functions, and it implies that adding bond functions in the calculation has a great effect on the interaction energies. We also find that with bond functions included in the CCSD(T)/aug-cc-pVDZ model chemistry, the potential energy minima are extremely close to the CBS limit and are better than the CCSD(T)/aug-cc-pVQZ values. Several levels of theory described in the text were used to determine pairwise analytic potential energy surfaces for Ar+CF₄. The analytic potential energy surfaces are in very good agreement with the ab initio values.     

Anomeric and rotameric preferences of glucopyranose in vacuo, water and organic solvents

Glucopyranose is the most stable form of glucose in solution. Identification of molecular structure of glucopyranose is very important because of its biological and synthetic significance; it is not an easy task because of the large number of possible configurations. Relative energies of exocyclic hydroxymethyl rotamers and α-β anomers of D-glucopyranose have been determined at the reference MP2/6-31G(d,p) level geometry by ab initio calculations at the infinite basis set limit of MP2 approach and with inclusion of CCSD(T) correction term evaluated with the aug-cc-pVDZ basis set in vacuum, water, dimethylsulfoxide, tetrahydrofurane and ethanol. The infinite basis set limit of MP2 level was determined by two point extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Solvent effects, relative energies and binding energies have been considered applying explicit calculations and implicit solvent models.     

Effect of microsolvation on zwitterionic glycine: an ab initio and density functional theory study

The effect of microsolvation on zwitterionic glycine, considering both (-NH3(+)) as proton donor and (-COO(-)) as proton acceptor at correlated ab initio (MP2) level and density functional methods (B3LYP, PW91, MPW1PW91 and PBE) using 6-311++G** basis set has been reported. DFT methods have been employed so as to compare the performance/quality of different gradient-corrected correlation functionals (PW91, PBE), hybrid functionals (B3LYP, MPW1PW91) and to predict the near quantitative structural and vibrational properties, at reduced computational cost. B3LYP method outperforms among the different DFT methods for the computed hydrogen bond distances and found closer to the value obtained by correlated MP2 level, whereas MPW1PW91 and PBE methods shows very similar values but approximately 0.03 A less, compared to B3LYP method. MP2 calculation and single point CCSD(T)//MP2 calculation have been considered to decompose the interaction energy, including corrections for basis set superposition error (BSSE). Moreover, charge distribution analysis has also been carried out to understand the long raised questions, how and why the two body energies have significant contribution to the total binding energy.     

Is 1-nitro-1-triazene a high energy density material?

An azo bridge (–N?=?N–) can not only desensitize explosives but also dramatically increase their heats of formation and explosive properties. Amino and nitro are two important high energy density functional groups. Here, we present calculations on 1-nitro-1-triazene (NH₂–N?=?N–NO₂). Thermal stability and detonation parameters were predicted theoretically at CCSD(T)/6-311G* level, based on the geometries optimized at MP2/6-311G* level. It was found that the p?→?π conjugation interaction and the intramolecular hydrogen bonding that exist in the system together increase the thermal stability of the molecule. Moreover, the detonation parameters were evaluated to be better than those of the famous HMX and RDX. Finally, the compound was demonstrated to be a high energy density material.     

Theoretical Ab initio study of the effects of methylation on the nature of hydrogen bonding in A:T base pair

We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pairs. Equilibrium geometries were obtained without symmetry restrictions by the gradient procedure at DFT level of theory with the standard 6-31G(d) basis set. Each local minima was verified by energy second derivative calculations. Single-point calculations for the DFT geometries have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stabilities and counterpoise corrected interaction energies are reported. In addition, using a variation-perturbation energy decomposition scheme, we have found the important contributions to the total interaction energy.     

Evaluation of density functional methods on the geometric and energetic descriptions of species involved in Cu+-promoted catalysis

We have evaluated the performance of 15 density functionals of diverse complexity on the geometry optimization and energetic evaluation of model reaction steps present in the proposed reaction mechanisms of Cu(I)-catalyzed indole synthesis and click chemistry of iodoalkynes and azides. The relative effect of the Cu⁺ ligand on the relative strength of Cu⁺-alkyne interactions, and the strong preference for a π-bonding mode is captured by all functionals. The best energetic correlations with MP2 are obtained with PBE0, M06-L, and PBE1PW91, which also provide good quality geometries. Furthermore, PBE0 and PBE1PW91 afford the best agreement with the high-level CCSD(T) computations of the deprotonation energies of Cu⁺-coordinated eneamines, where MP2 strongly disagrees with CCSD(T) and the examined DFT functionals. PBE0 also emerged as the most suitable functional for the study of the energetics and geometries of Cu⁺ hydrides, while at the same time correctly capturing the influence of the Cu⁺ ligands on the metal reactivity.     

Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation

A comparison is made of the relative accuracy of some NDDO semiempirical methods and the DFT functionals LYP and PW91 using both double and triple zeta basis sets. The comparison is between the calculated heat of formation and that reported in the NIST database.Electronic Supplementary Material Parameters for the tailored method are available in the supplementary material; these are suitable for use with MOPAC2002. All raw data (experimental heats of formation, geometries, total energies and heats of formation for the various methods, etc.) are also provided in CAChe format. Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.     

Quantum-mechanical computations on the electronic structure of trans-resveratrol and trans-piceatannol: a theoretical study of the stacking interactions in trans-resveratrol dimers

Accurate quantum-chemical calculations based on the second-order M?ller-Plesset perturbation method (MP2) and density functional theory (DFT) were performed for the first time to investigate the electronic structures of trans-resveratrol and trans-piceatannol, as well as to study the stacking interaction between trans-resveratrol molecules. Ab initio MP2 calculations performed with using standard split-valence Pople basis sets led us to conclude that these compounds have structures that deviate strongly from planarity, whereas the DFT computations for the same basis sets revealed that the equilibrium geometries of these bioactive polyphenols are planar. Furthermore, the results obtained at the MP2(full)/aug-cc-pVTZ and B3LYP/aug-cc-pVTZ levels indicated that the geometries of trans-resveratrol and trans-piceatannol are practically planar at their absolute energy minima. The relative energies of the equilibrium geometries of trans-resveratrol on its potential energy surface were computed at the MP2(full)/aug-cc-pVTZ level. According to the results obtained, a T-shaped (edge-to-phase) conformer of trans-resveratrol dimer is the most stable in vacuum. This T-shaped conformer is mainly stabilized by strong hydrogen bonding and weak C-H...π interactions. Stacked structures with parallel-displaced trans-stilbene skeletons were also found to be energetically stable. The vertical separation and twist angle dependencies of the stacking energy were investigated at the MP2(full)/aug-cc-pVTZ, B3LYP/aug-cc-pVTZ, and HF/aug-cc-pVTZ levels. The standard B3LYP functional and the Hartree-Fock method neglect long-range attractive dispersion interactions. The MP2 computations revealed that the London dispersion energy cannot be neglected at long or short distances. The stacked model considered here may be useful for predicting the quantum nature of the interactions in π-stacked systems of other naturally occurring stilbenoids, and can help to enhance our understanding of the antioxidant and anticancer activities of trans-resveratrol.     

Ab initio study of weakly bound halogen complexes: RX⋯PH3

Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R = methyl, phenyl, acetyl, H and X = F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX?PH₃. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range ?4.14 to ?11.92 kJ mol^?1 (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27 % in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl?PH₃ and all MeX?PH₃ complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7–6.7 u.a. (about 3–7 %).     

Exploring the potential energy surface of novel [H,S, Se,Br] species: a high level first principle study

The characterization of the seleno-sulfide-bromo systems and the isomerization process on the [H, S, Se, Br] potential energy surface were investigated using state-of-the-art theoretical methods. The CCSD(T) and the MP2 levels of theory were employed along with the series of correlation consistent basis sets extrapolated to the complete basis set (CBS) limit in the optimization of the geometrical parameters and computation of electronic energies. The relative stability, in kcal mol^?1, at the CCSD(T)/CBS follows the trend: HSSeBr (0) > HSeSBr (9.51) > SSeHBr (24.02) > SeSHBr (25.42). This order was observed in the previous study of the [H, S, Se, Cl] species. The structural parameters and vibrational frequencies of the [H, S, Se, Br] species are reported. This research work should be helpful to experimentalists in order to gain insights into these novel heteroatom molecules.

Open image in new window

Graphical abstract Relative energy profile (in kcal mol^?1) using the CCSD(T)/CBS and MP2/CBS (in parentheses) method of the stationary states on the [H, S, Se, Br] PES.

     

The reaction of the aminoboranylidene-iminoborane isomerization: a CASSCF direct dynamics study

The barrier and the potential-energy surface of the isomerization from aminoboranylidene (BNH₂) to iminoborane (HBNH) have been studied using complete active space self-consistent field (CASSCF) with the 6−31+G(d, p) basis set and higher-level energy methods. The rate constants of the isomerization reaction are reported by employing the direct ab initio dynamics method. The geometries of all the stationary points were optimized using the B3LYP and CCSD methods with the cc-pVTZ and cc-pVQZ basis sets. The information along the intrinsic reaction coordinate (IRC) was also calculated at the CASSCF/6−31+G (d,p) level of theory. The energies were refined at the G3, G3MP2, G3MP2B3, CBS-Q, CBS-QB3, and two high-level (HL) methods based on the geometries optimized using CASSCF/6-31+G(d,p). The rate constants were evaluated using conventional transition-state theory (TST), canonical variational transition-state theory (CVT), and canonical variational transition-state theory with small curvature tunneling correction (CVT/SCT) and conventional transition-state theory with Eckart tunneling correction (TST/Eckart). According to the calculated results, we conclude that the tunneling effect is very important to this isomerization reaction.     

Ab Initio and DFT Study of the Structures,Vibrations and Energetics of the Urea Dimer and Trimer

Stable structures and electronic properties of small urea clusters are investigated with ab initio calculations. We optimized the cluster geometries and calculated the vibrational frequencies with Hartree–Fock (HF), second-order Møller-Plesset perturbation theory (MP2), and Density Functional Theory (DFT) methods using different basis sets. The most stable dimer was found to consist of two nonplanar urea molecules which are connected by two N–-H...O bonds in a common plane, and the most stable trimer has a flat structure of complex and planar C2 form for each urea molecule, like in the crystal. The interaction energies were corrected for the basis set superposition error (BSSE) using the full Boys*ndash;Bernardi counterpoise correction scheme. The stability of different dimer and trimer structures, the features of formation of H-bonds and presented here are compared to the available experimental data.     

Theoretical study on the mechanism of cycloaddition reaction between silylene silylene(H2Si=Si:) and acetaldehyde

The mechanism of the cycloaddition reaction between singlet silylene silylene (H(2)Si=Si:) and acetaldehyde has been investigated with CCSD(T)//MP2/6-31G* and CCSD(T)//MP2/6-31G** method, from the potential energy profile, we could predict that the reaction has three competitive dominant reaction pathways. The present rule of this reaction is that the 3p unoccupied orbital of the Si: atom in silylene silylene (H(2)Si=Si:) inserts on the π orbital of acetaldehyde from oxygen side, resulting in the formation of an intermediate. Isomerization of the intermediate further leads to the generation of a four-membered ring silylene (the H(2)Si-O in the opposite position). In addition, the [2?+?2] cycloaddition reaction of the two π-bonds in silylene silylene and acetaldehyde generates another four-membered ring silylene (the H(2)Si-O in the syn-position). Because of the unsaturated property of Si: atom in the two four-membered ring silylenes, they could further react with acetaldehyde, resulting in the generation of two spiro-heterocyclic ring compounds with Si. Simultaneously, the ring strain of the four-membered ring silylene (the H(2)Si-O in the syn-position) makes it isomerize to a twisted four-membered ring product.     

Many-body energies during proton transfer in an aqueous system

The energetics of the mechanism of proton transfer from a hydronium ion to one of the water molecules in its first solvation shell are studied using density functional theory and the Møller–Plesset perturbation (MP2) method. The potential energy surface of the proton transfer mechanism is obtained at the B3LYP and MP2 levels with the 6-311++G** basis set. Many-body analysis is applied to the proton transfer mechanism to obtain the change in relaxation energy, two-body, three-body and four-body energies when proton transfer occurs from the hydronium ion to one of the water molecules in its first solvation shell. It is observed that the binding energy (BE) of the complex decreases during the proton transfer process at both levels of theory. During the proton transfer process, the % contribution of the total two-body energy to the binding energy of the complex increases from 62.9 to 68.09% (39.9 to 45.95%), and that of the total three-body increases from 25.9 to 27.09% (24.16 to 26.17%) at the B3LYP/6-311++G** (MP2/ 6-311++G**) level. There is almost no change in the water–water–water three-body interaction energy during the proton transfer process at both levels of theory. The contribution of the relaxation energy and the total four-body energy to the binding energy of the complex is greater at the MP2 level than at the B3LYP level. Significant differences are found between the relaxation energies, the hydronium–water interaction energies and the four-body interaction energies at the B3LYP and MP2 levels.     

Theoretical studies of the interaction between enflurane and water

Increase of the atmospheric concentration of halogenated organic compounds is partially responsible for a change of the global climate. In this work we have investigated the interaction between halogenated ether and water, which is one of the most important constituent of the atmosphere. The structures of the complexes formed by the two most stable conformers of enflurane (a volatile anaesthetic) with one and two water molecules were calculated by means of the counterpoise CP-corrected gradient optimization at the MP2/6–311++G(d,p) level. In these complexes the CH…O_w hydrogen bonds are formed, with the H…O_w distances varying between 2.23 and 2.32 Å. A small contraction of the CH bonds and the blue shifts of the ν(CH) stretching vibrations are predicted. There is also a weak interaction between one of the F atoms and the H atom of water, with the H_w…F distances between 2.41 and 2.87 Å. The CCSD(T)/CBS calculated stabilization energies in these complexes are between ?5.89 and ?4.66 kcal?mol^?1, while the enthalpies of formation are between ?4.35 and ?3.22 kcal?mol^?1. The Cl halogen bonding between enflurane and water has been found in two complexes. The intermolecular (Cl···O) distance is smaller than the sum of the corresponding van der Waals radii. The CCSD(T)/CBS stabilization energies for these complexes are about ?2 kcal?mol^?1.

An improved generalized AMBER force field (GAFF) for urea

We describe an improved force field parameter set for the generalized AMBER force field (GAFF) for urea. Quantum chemical computations were used to obtain geometrical and energetic parameters of urea dimers and larger oligomers using AM1 semiempirical MO theory, density functional theory at the B3LYP/6-31G(d,p) level, MP2 and CCSD ab initio calculations with the 6-311++G(d,p), aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets, and with the CBS-QB3 and CBS-APNO complete basis set methods. Seven different urea dimer structures were optimized at the MP2/aug-cc-pVDZ level to obtain accurate interaction energies. Atomic partial charges were calculated at the MP2/aug-cc-pVDZ level with the restrained electrostatic potential (RESP) fitting approach. The interaction energies computed with these new RESP charges in the force field are consistent with those obtained from CCSD and MP2 calculations. The linear dimer structure calculated using the force field with modified geometrical parameters and the new RESP charge set agrees well with available experimental data.     

Variation of reaction dynamics for OH hydrogen abstraction from glycine between ab initio levels of theory

The variation in reaction dynamics of OH hydrogen abstraction from glycine between HF, MP2, CCSD(T), M05-2X, BHandHLYP, and B3LYP levels was demonstrated. The abstraction mode shows distinct patterns between these five levels and determines the barrier height, and the spin density transfer between OH radical and glycine. These differences are mainly resulted from the spin density distribution and geometry of the alpha carbon during the abstraction. The captodative effect which is commonly believed as one of the major factors to stabilize the caron-centered radical can only be observed in DFT levels but not in HF and MP2 levels. Difference in the abstraction energy were found in these calculation levels, by using the result of CCSD(T) as reference, B3LYP, BHandHLYP, and M05-2X underestimated the reaction barrier about 5.1, 0.1, and 2.4 kcal mol^-1, while HF and MP2 overestimated 19.1 kcal mol^-1 and 1.6 kcal mol^-1, respectively. These differences can be characterized by the vibration mode of imaginary frequency of transition states, which indicates the topology around transition states and determines reaction barrier height. In this model system, BHandHLYP provides the best prediction of the energy barrier among those tested methods.     

New insights into the molecular basis of lectin-carbohydrate interactions: A calorimetric and structural study of the association of hevein to oligomers of N-acetylglucosamine

Isothermal titration calorimetry was used to characterize thermodynamically the association of hevein, a lectin from the rubber tree latex, with the dimer and trimer of N-acetylglucosamine (GlcNAc). Considering the changes in polar and apolar accessible surface areas due to complex formation, we found that the experimental binding heat capacities can be reproduced adequately by means of parameters used in protein-unfolding studies. The same conclusion applies to the association of the lectin concanavalin A with methyl-α-mannopyranoside. When reduced by the polar area change, binding enthalpy values show a minimal dispersion around 100°C. These findings resemble the convergence observed in protein-folding events; however, the average of reduced enthalpies for lectin-carbohydrate associations is largely higher than that for the folding of proteins. Analysis of hydrogen bonds present at lectin-carbohydrate interfaces revealed geometries closer to ideal values than those observed in protein structures. Thus, the formation of more energetic hydrogen bonds might well explain the high association enthalpies of lectin-carbohydrate systems. We also have calculated the energy associated with the desolvation of the contact zones in the binding molecules and from it the binding enthalpy in vacuum. This latter resulted 20% larger than the interaction energy derived from the use of potential energy functions. Proteins 29:467–477, 1997. © 1997 Wiley-Liss, Inc.     

The investigation of hydrocarbon cracking reaction energetics with composite energy methods

Hydrocarbo cracking reactions are one of the most commonly encountered reactions in the petroleum industry, and the energetics of the reactions are crucial in understanding the reaction mechanisms and predicting reaction rates. In this work, a modified composite energy method (CBS-RAD(MP2)) is created as a version of the CBS-RAD method which gives accurate energetics for hydrocarbon free radical reactions. It replaces the time consuming QCISD(fc)/6-31g* method in the geometry optimization and frequency calculation steps with MP2(full)/6-31g* level calculations. The accuracy of the new CBS-RAD(MP2) method is compared with the widely used G2, G3 and CBS-QB3 composite methods for predicting heats of reaction and activation barriers of 14 hydrocarbon cracking reactions. We find that the new CBS-RAD(MP2) method has the second least RMS error of 1.22 kcal/mol for heats of reaction calculations. For activation energy calculations, the new CBS-RAD(MP2) method has the least RMS error of 1.37 kcal/mol. Moreover, the CBS-RAD(MP2) method was found to require only 81% of the computational time required compared to the CBS-QB3 method, 32% of G3 and 15% of the G2 method, making it an attractive alternative for predicting hydrocarbon cracking reaction energetics.     

Characteristics and nature of the intermolecular interactions in boron-bonded complexes with carbene as electron donor: an <Emphasis Type="Italic">ab initio</Emphasis>, SAPT and QTAIM study

We report geometries, stabilization energies, symmetry adapted perturbation theory (SAPT) and quantum theory of atoms in molecules (QTAIM) analyses of a series of carbene–BX₃ complexes, where X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br. The stabilization energies were calculated at HF, B3LYP, MP2, MP4 and CCSD(T)/aug-cc-pVDZ levels of theory using optimized geometries of all the complexes obtained from B3LYP/aug-cc-pVTZ. Quantitatively, all the complexes indicate the presence of B–C_carbene interaction due to the short B–C_carbene distances. Inspection of stabilization energies reveals that the interaction energies increase in the order NH₂ > OH > CH₃ > F > H > Cl > Br > NC > CN, which is the opposite trend shown in the binding distances. Considering the SAPT results, it is found that electrostatic effects account for about 50% of the overall attraction of the studied complexes. By comparison, the induction components of these interactions represent about 40% of the total attractive forces. Despite falling in a region of charge depletion with ∇² ρ _BCP >0, the B–C_carbene bond critical points (BCPs) are characterized by a reasonably large value of the electron density (ρ _BCP) and H_BCP <0, indicating that the potential energy overcomes the kinetic energy density at BCP and the B–C_carbene bond is a polar covalent bond.