Computational thermochemistry of glycolaldehyde

We use a variant of the focal point analysis to refine estimates of the relative energies of the four low‐energy torsional conformers of glycolaldehyde. The most stable form is the cis‐cis structure which enjoys a degree of H‐bonding from hydroxyl H to carbonyl O; here dihedral angles τ₁ (O?C? C? O) and τ₂ (C? C? O? H) both are zero. We optimized structures in both CCSD(T)/aug‐cc‐pVDZ and aug‐cc‐pVTZ; the structures agree within 0.01 Å for bond lengths and 1.0 degrees for valence angles, but the larger basis brings the rotational constants closer to experimental values. According to our extrapolation of CCSD(T) energies evaluated in basis sets ranging to aug‐cc‐pVQZ the trans‐trans form (180°, 180°) has a relative energy of 12.6 kJ/mol. The trans‐gauche conformer (160°, ±75°) is situated at 13.9 kJ/mol and the cis‐trans form (0°, 180°) at 18.9 kJ/mol. Values are corrected for zero point vibrational energy by MP2/aug‐cc‐pVTZ frequencies. Modeling the vibrational spectra is best accomplished by MP2/aug‐cc‐pVTZ with anharmonic corrections. We compute the Watsonian parameters that define the theoretical vibrational‐rotational spectra for the four stable conformers, to assist the search for these species in the interstellar medium. Six transition states are located by G4 and CBS‐QB3 methods as well as extrapolation using energies for structures optimized in CCSD(T)/aug‐cc‐pVDZ structures. We use two isodesmic reactions with two well‐established thermochemical computational schemes G4 and CBS‐QB3 to estimate energy enthalpy and Gibbs energy of formation as well as the entropy of the gas phase system. Our extrapolated electronic energies of species appearing in the isodesmic reactions produce independent values of thermodynamic quantities consistent with G4 and CBS‐QB3. © 2013 Wiley Periodicals, Inc.     

Highly Accurate CCSD(T) and DFT–SAPT Stabilization Energies of H‐Bonded and Stacked Structures of the Uracil Dimer

The CCSD(T) interaction energies for the H‐bonded and stacked structures of the uracil dimer are determined at the aug‐cc‐pVDZ and aug‐cc‐pVTZ levels. On the basis of these calculations we can construct the CCSD(T) interaction energies at the complete basis set (CBS) limit. The most accurate energies, based either on direct extrapolation of the CCSD(T) correlation energies obtained with the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets or on the sum of extrapolated MP2 interaction energies (from aug‐cc‐pVTZ and aug‐cc‐pVQZ basis sets) and extrapolated ΔCCSD(T) correction terms [difference between CCSD(T) and MP2 interaction energies] differ only slightly, which demonstrates the reliability and robustness of both techniques. The latter values, which represent new standards for the H‐bonding and stacking structures of the uracil dimer, differ from the previously published data for the S22 set by a small amount. This suggests that interaction energies of the S22 set are generated with chemical accuracy. The most accurate CCSD(T)/CBS interaction energies are compared with interaction energies obtained from various computational procedures, namely the SCS–MP2 (SCS: spin‐component‐scaled), SCS(MI)–MP2 (MI: molecular interaction), MP3, dispersion‐augmented DFT (DFT–D), M06–2X, and DFT–SAPT (SAPT: symmetry‐adapted perturbation theory) methods. Among these techniques, the best results are obtained with the SCS(MI)–MP2 method. Remarkably good binding energies are also obtained with the DFT–SAPT method. Both DFT techniques tested yield similarly good interaction energies. The large magnitude of the stacking energy for the uracil dimer, compared to that of the benzene dimer, is explained by attractive electrostatic interactions present in the stacked uracil dimer. These interactions force both subsystems to approach each other and the dispersion energy benefits from a shorter intersystem separation.     

Improving on equilibrium isotropic nuclear shielding constants

Isotropic nuclear shielding constants at the equilibrium molecular structure σ_eq and zero‐point vibrational corrections (ZPVCs) to σ_eq are evaluated using the B3LYP/aug‐cc‐pVTZ level of theory, as well as the KT2/aug‐cc‐pVTZ level of theory. Various scaling factors and systematic corrections are obtained by linear regression to experimental shielding constants. Comparisons of the scaled and systematically corrected equilibrium and vibrationally averaged shielding constants reveal that, at the 99% confidence level, the ZPVCs via second‐order perturbation theory do not improve the agreement of B3LYP/aug‐cc‐pVTZ and KT2/aug‐cc‐pVTZ calculated shielding constants with experiment. This holds true when the same analysis is applied to CCSD(T)/aug‐cc‐pCV[TQ]Z calculated σ_eq of Teale et al. [Journal of Chemical Physics 2013, 138, 024111]. In addition, at the 99% confidence level, B3LYP/aug‐cc‐pVTZ and KT2/aug‐cc‐pVTZ scaled and systematically corrected shielding constants are found to be statistically no different from CCSD(T)/aug‐cc‐pCV[TQ]Z calculated σ_eq. The use of scaling factors and systematic corrections could thus provide a cheaper but yet reasonably accurate alternative for the study of nuclear shielding constants of larger systems.     

Structural and vibrational analysis of the OH torsional motion in difluorohydroxyborane

In this work, we present a complete structural and vibrational analysis of the OH torsional motion in difluorohydroxyborane (BF₂OH) at the HF/aug‐cc‐pVTZ, MP2(full)/aug‐cc‐pVTZ, and CCSD/aug‐cc‐pVTZ theory levels. After full relaxation of the geometry, the equilibrium structure is found in a planar conformation of C_s symmetry. The difference in the two BF distances suggests the existence of a nonbonded interaction between the fluorine and oxygen atoms. The structural and energetic variation of BF₂OH as a function of the OH torsional angle is considered. The torsional barrier, at the CCSD/aug‐cc‐pVTZ level, and including the effect of the zero‐point energy of the remaining vibrations, is found 2,728 cm^?1. In addition, an anharmonic Hamiltonian for the OH torsional mode is presented and variationally solved. To simplify the treatment and to classify the energy levels, BF₂OH is classified under a G₄ nonrigid group accounting for the inversion symmetry of the molecule and the interchange of the fluorine atoms. The computed torsional energy levels exhibit a very small inversion splitting. The torsional spectrum is simulated considering the dipole moment components along the principal axes of inertia as an explicit function of the torsional coordinate. We observe three dominant bands in the spectrum formed by doublets corresponding to ν₉ = 0 → 1, 2 transitions. The fundamental is an a‐type, Franck–Condon, transition. This is the strongest and appears at 466.80 cm^?1 with relative intensity 0.4312. The ν₉ = 0 → 2 bands correspond to doublets of b‐ and c‐type, i.e., Herzberg–Teller transitions. These are two overlapping bands found at 890.92 and 890.94 cm^?1 with intensity 0.2207 for the b‐type band and 0.2193 for the c‐type band. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Different Catalytic Effects of a Single Water Molecule: The Gas‐Phase Reaction of Formic Acid with Hydroxyl Radical in Water Vapor

The effect of a single water molecule on the reaction mechanism of the gas‐phase reaction between formic acid and the hydroxyl radical was investigated with high‐level quantum mechanical calculations using DFT–B3LYP, MP2 and CCSD(T) theoretical approaches in concert with the 6‐311+G(2df,2p) and aug‐cc‐pVTZ basis sets. The reaction between HCOOH and HO has a very complex mechanism involving a proton‐coupled electron transfer process (pcet), two hydrogen‐atom transfer reactions (hat) and a double proton transfer process (dpt). The hydroxyl radical predominantly abstracts the acidic hydrogen of formic acid through a pcet mechanism. A single water molecule affects each one of these reaction mechanisms in different ways, depending on the way the water interacts. Very interesting is also the fact that our calculations predict that the participation of a single water molecule results in the abstraction of the formyl hydrogen of formic acid through a hydrogen atom transfer process (hat).     

Highly accurate relativistic universal Gaussian basis set for Dirac–Fock–Breit calculations

Ion mobilities of H₂O⁺ drifting in helium are calculated and compared with experiment. These calculations employ global potential energy surfaces of the H₂O⁺–He complex, which in the present case were calculated ab initio at the unrestricted MP2 level of theory using a basis set of aug‐cc‐pVTZ quality, and treating the ion as a rigid body. Details are presented of the general characteristics of both the ground and first‐excited electronic states of the complex. Although only the ground‐state surface was used for the mobility calculations, the ab initio determination of the ground state necessitated the inclusion of the first‐excited state owing to the presence of a crossing between the two. This crossing is also described. Mobilities calculated from the global surfaces are in good agreement with experiment. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical investigation of the structures and spectroscopic properties of (H2O4)n (n = 1–4) clusters

Density functional theory and ab initio calculations were performed to elucidate the hydrogen interactions in (H₂O₄)_n (n = 1–4) clusters. The optimized geometries, binding energies, and harmonic vibrational frequencies were predicted at various levels of theory. The trans conformer of the H₂O₄ monomer was predicted to be the most stable structure at the CCSD(T)/aug‐cc‐pVTZ level of theory. The binding energies per H₂O₄ monomer increased in absolute value by 9.0, 10.1, and 11.8 kcal/mol from n = 2 to n = 4 at the MP2/cc‐pVTZ level of theory (after the zero‐point vibrational energy and basis set superposition error corrections). This result implies that the intermolecular hydrogen bonds were stronger in the long‐chain clusters, that is, the formation of the longer chain in the (H₂O₄)_n clusters was more energetically favorable.     

A Theoretical Study of the Kinetics of the Hydrogen Atom Abstraction Reactions from Cyclopropane by H,O (3P), and Cl (2P3/2) Atoms and OH Radicals

The rate constants of the H‐abstraction reactions from cyclopropane by H, O (³P), Cl (²P_3/2), and OH radicals have been calculated over the temperature range of 250?2500 K using two different levels of theory. Calculations of optimized geometrical parameters and vibrational frequencies are performed using the MP2 method combined with the cc‐pVTZ basis set and the 6–311++G(d,p) basis set. Single‐point energy calculations have been carried out with the highly correlated ab initio coupled cluster method in the space of single, double, and triple (perturbatively) electron excitations CCSD(T) using either the cc‐pVTZ, aug‐cc‐pVTZ, and aug‐cc‐pVQZ basis sets or the 6–311++G(3df,3pd) basis set. The CCSD(T) calculated potential energies have been extrapolated to the complete basis limit (CBS) limit. The Full Configuration Interaction (FCI) energies have been also estimated using the continued‐fraction approximation as proposed by Goodson (J. Chem. Phys., 2002, 116, 6948–6956). Canonical transition‐state theory combined with an Eckart tunneling correction has been used to predict the rate constants as a function of temperature using two kinetic models (direct abstraction or complex mechanism) at two levels of theory (CCSD(T)‐cf/CBS//MP2/cc‐pVTZ and CCSD(T)‐cf/6–311++G(3df,3pd)//MP2/6–311++G(d,p)). The calculated kinetic parameters are in reasonable agreement with their literature counterparts for all reactions. In the light of these trends, the use of the Pople‐style basis sets for studying the reactivity of other systems such as larger cycloalkanes or halogenated cycloalkanes is recommended because the 6–311++G(3df,3pd) basis set is less time consuming than the aug‐cc‐pVQZ basis set. Based on our calculations performed at the CCSD(T)‐cf/CBS//MP2/cc‐pVTZ level of theory, the standard enthalpy of formation at 298 K for the cyclopropyl radical has been reassessed and its value is (290.5 ± 1.6) kJ mol^?1.     

Ab Initio and Quantum Chemical Topology studies on the isomerization of HONO to HNO2. Effect of the basis set in QCT

The article focus on the isomerization of nitrous acid HONO to hydrogen nitryl HNO₂. Density functional (B3LYP) and MP2 methods, and a wide variety of basis sets, have been chosen to investigate the mechanism of this reaction. The results clearly show that there are two possible paths: 1) Uncatalysed isomerisation, trans‐HONO → HNO₂, involving 1,2‐hydrogen shift and characterized by a large energetic barrier 49.7 ÷ 58.9 kcal/mol, 2) Catalysed double hydrogen transfer process, trans‐HONO + cis‐HONO → HNO₂ + cis‐HONO, which displays a significantly lower energetic barrier in a range of 11.6 ÷ 18.9 kcal/mol. Topological analysis of the Electron Localization Function (ELF) shows that the hydrogen transfer for both studied reactions takes place through the formation of a ‘dressed’ proton along the reaction path. 1 Use of a wide variety of basis sets demonstrates a clear basis set dependence on the ELF topology of HNO₂. Less saturated basis sets yield two lone pair basins, V₁(N), V₂(N), whereas more saturated ones (for example aug‐cc‐pVTZ and aug‐cc‐pVQZ) do not indicate a lone pair on the nitrogen atom. Topological analysis of the Electron Localizability Indication (ELI‐D) at the CASSCF (12,10) confirms these findings, showing the existence of the lone pair basins but with decreasing populations as the basis set becomes more saturated (0.35e for the cc‐pVDZ basis set to 0.06e for the aug‐cc‐pVTZ). This confirms that the choice of basis set not only can influence the value of the electron population at the particular atom, but can also lead to different ELF topology. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Silicon amino acids

The existence and gas phase stability of silicon analogues of three natural amino acids (i.e., silicon glycine, silicon alanine, and silicon valine) belonging to the novel class of compounds termed silicon amino acids (SiAA) are investigated theoretically on the basis of ab initio QCISD/aug‐cc‐pVTZ and MP2/aug‐cc‐pVTZ calculations. All molecules studied (in their gas phase canonical forms) are structurally comparable to their proteinogenic counterparts (i.e., glycine, l ‐alanine, and l ‐valine) and capable of forming several structural isomers as such. These higher energy isomers are characterized by small relative energies (not exceeding 4 kcal mol⁻¹). The simulated IR spectra of the Si‐Gly, Si‐Ala, and Si‐Val global minima are also presented and discussed.     

Tetrel bonds between PhSiF3/PhTH3 (T = Si,Ge, Sn) and H3ZO (Z = N,P, As): A pentacoordinate silicon (IV) complex

The nature of the complexes PhTH₃ H₃ZO and PhSiF₃ H₃ZO (T = Si, Ge, and Sn; Z = N, P, and As) has been investigated at the MP2/aug’‐cc‐pVTZ(PP) level. These complexes are primarily stabilized by one T···O tetrel bond. Interaction energies of these complexes vary from 11 to 220 kJ/mol, and T···O separations from 1.89 to 3.09 Å. Charge transfer from the O lone pair into the C T and T H σ* antibonding orbitals leads to the stabilization of these complexes. The T···O tetrel bond between PhTH₃/PhSiF₃ and H₃NO exhibits a significant degree of covalence, characterized by the large interaction energy, negative energy density, and large charge transfer. Furthermore, a pentacoordinate silicon (IV) complex is formed in PhSiF₃ H₃NO with the Si···O distance almost close to the length of Si O bond. This indicates that the oxygen atom in N‐oxides shows a strong affinity to the silicon atom in organosilicon compounds.     

An electronic structure theory investigation of the physical chemistry of the intermolecular complexes of cyclopropenylidene with hydrogen halides

The proton accepting and donating abilities of cyclopropenylidene (c‐C₃H₂) on its complexation with hydrogen halides H? X (X = F, Cl, Br) are analyzed using density‐functional theory with three functionals (PBE0, B3LYP, and B3LYP‐D) and benchmarked against second‐order Møller–Plesset (MP2) theory. Standard signatures including, inter alia, dipole moment enhancement, charge transfer from the carbenic lone pair to the antibonding σ*(H? X) orbital, and H? X bond elongation are examined to ascertain the presence of hydrogen bonding in these complexes. The latter property is found to be accompanied with a pronounced red shift in the bond stretching frequency and with a substantial increase in the infrared intensity of the band on complex formation. The MP2/aug‐cc‐pVTZ c‐C₃H₂···H? F complex potential energy surface turns out to be an asymmetric deep single well, while asymmetric double wells are found for the c‐C₃H₂···H? Cl and c‐C₃H₂···H? Br complexes, with an energy barrier of 4.1 kcal mol^?1 for proton transfer along the hydrogen bond in the latter complex. Hydrogen‐bond energy decomposition, with the reduced variational space self‐consistent field approach, indicates that there are large polarization and charge‐transfer interactions between the interacting partners in c‐C₃H₂···H? Br compared to the other two complexes. The C···H bonds are found to be predominantly ionic with partial covalent character, unveiled by the quantum theory of atoms in molecules. The present results reveal that the c‐C₃H₂ carbene divalent carbon can act as a proton acceptor and is responsible for the formation of hydrogen bonds in the complexes investigated. © 2012 Wiley Periodicals, Inc.     

ChemInform Abstract: Smallest Deltahedra Silicon Dicarbide: C2Si32‐.

A total of 20 singlet and 36 triplet C₂Si₃^2‐ isomers are obtained by quantum chemical calculations at the B3LYP/aug‐cc‐pVTZ level.     

Ab initio study of the structure,cooperativity, and vibrational properties in the mixed hydrogen‐bonded trimers of hydrogen isocyanide and water

The five trimers of H₂O···HNC···H₂O, H₂O···H₂O···HNC, HNC···H₂O···H₂O, H₂O···HNC···HNC, and HNC···HNC···H₂O have been studied with quantum chemical calculations. Their structures, harmonic vibrational frequencies and interaction energies have been calculated at the B3LYP and MP2 levels with the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets. The cooperative effect on these properties has also been studied quantitatively. For HNC:(H₂O)₂ systems, the cyclic H₂O···H₂O···HNC trimer is most stable with an interaction energy of ?16.01 kcal/mol and a large cooperative energy of ?3.25 kcal/mol at the MP2/aug‐cc‐pVTZ level. For H₂O:(HNC)₂ systems, the interaction energy and cooperative energy in the H₂O···HNC···HNC trimer are larger than those in the HNC···HNC···H₂O trimer. The NH stretch frequency has a blue shift for the terminal HNC molecule in the HNC···H₂O···H₂O and HNC···HNC···H₂O trimers and a red shift in other cases. A many‐body analysis has also been performed to understand the interaction energies in these hydrogen‐bonded clusters. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

F2 dimer: Improved intermolecular potential energy surface using ab initio calculations

A computational study on the intermolecular potential energy of 44 different orientations of F₂ dimers is presented. Basis set superposition error (BSSE) corrected potential energy surface is calculated using the supermolecular approach at CCSD(T) and QCISD(T) levels of theory. The interaction energies obtained using the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets are extrapolated to the complete basis set limit using the latest extrapolation scheme. The basis set effect is checked and it is found that the extrapolated intermolecular energies provide the best compromise between the accuracy and computational cost. Among 1320 energy points of F₂–F₂ system covering more relative orientations, the most stable structure of the dimers was obtained with a well depth of ?146.62 cm^?1 that related to cross configuration, and the most unstable structure is related to linear orientation with a well depth of ?52.63 cm^?1. The calculated second virial coefficients are in good agreement with experimental data. The latest extrapolation scheme of the complete basis set limit at the CCSD(T) level of theory is used to determine the intermolecular potential energy surface of the F₂ dimer. Comparing the results obtained by the latest scheme with those by older schemes show that the new approach provides the best compromise between accuracy and computational cost.     

Many-body interaction in glycine-(water)3 complex using density functional theory method

Various configurations were investigated to find the most stable structures of glycine-(water)3 complex. Five different optimized conformers of glycine-(water)3 complex are obtained from density functional theory calculations using 6-311++G* basis set. Relaxation energy and many body interaction energies (two, three, and four body) are also calculated for these conformers. Out of the five conformers, the most stable conformer has the BSSE corrected total energy -513.917 967 7 Hartree and binding energy -27.28 Kcal/mol. It has been found that the relaxation energies, two body energies and three body energies have significant contribution to the total binding energy whereas four body energies are very small. The chemical hardness and chemical potential also confirmed the stability of the conformer having lowest total energy.     

Electronic Structure Trends in N‐Heterocyclic Carbenes (NHCs) with Varying Number of Nitrogen Atoms and NHC?Transition‐Metal Bond Properties

Carbenes derived from five‐membered heterocycles with different numbers of nitrogen atoms ranging from two to four lead formally either to normal N‐heterocyclic or mesoionic carbenes with, in some cases, the same skeletal structure. The electronic structures of fourteen of these compounds were examined by means of DFT calculations at the B3LYP/aug‐cc‐pVTZ level. The examined parameters include the energies of the σ‐lone pair at C_carbene and the π‐HOMO of the protonated form, which are correlated to the first and second proton affinities. The singlet–triplet energy gap was used as a measure of the stability of the N‐heterocyclic carbene (NHC) towards dimerisation. Natural population analysis provided insight into the variation of the p_π population and the natural charge at C_carbene with NHC structure. Additionally, the transition metal? NHC bond in L‐AuCl and L‐TiCl₄ and the nature of the orbital interactions between the NHC and the transition‐metal fragment were analysed in detail by the extended transition state–natural orbitals for chemical valence (ETS–NOCV) approach at the BP86/TZ2P level. Similarities and differences between the NHC? gold and the NHC? titanium bond are discussed, and trends in key bonding properties can be traced back to the variation of the electronic parameters of the NHC.     

New global potential energy surface of the MgH2 system and dynamics studies of the reaction H + MgH → Mg + H2

A new global potential energy surface for the ground state of MgH₂ was constructed using the permutation invariant polynomial neural network method. About 70 000 ab initio energy points were calculated via the multi‐reference configuration interaction method method with aug‐cc‐pVTZ and aug‐cc‐pVQZ basis sets, and these points were used to construct the potential energy surface (PES). To avoid basis set superposition error, the basis set was extrapolated to the complete basis set limit using the two point energy extrapolation formula. The root mean square error of the present PES is only 8.85 meV. Initial state (v = 0, j = 0) dynamics studies were performed using the time‐dependent wave packet method with a second‐order split operator for the total angular momentum J up to a value of 50. Furthermore, the reaction probability, integral cross section, and thermal rate constant are reported and compared with available theoretical studies.     

Multipolar electrostatics for proteins: Atom–atom electrostatic energies in crambin

Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom‐atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom‐atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ?_A+ ?_B + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom‐atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug‐cc‐pVTZ and MP2/aug‐cc‐pVTZ levels are only slightly larger than those calculated at HF/6‐31G(d,p) level. This convergence behavior is transferable to the well‐known amyloid beta polypeptide Aβ_1–42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance. © 2013 Wiley Periodicals, Inc.     

Many‐body interactions of carbon monoxide cyclic oligomers: A computational study

Structural properties and energetics for the optimized carbon monoxide cyclic oligomers are analyzed at the correlated ab initio second‐order Møller–Plesset (MP2) and density functional methods (B3LYP and mPW1PW), using Dunning's cc‐pVXZ (X = D, T, Q) basis set, augmented with diffuse functions. Many‐body interactions of the stable carbon monoxide cyclic oligomers, (CO)₄ and (CO)₅ are computed at the MP2/aug‐cc‐pVTZ level. Contributions of two‐ to five‐body terms to each of these oligomers for their interaction energies, including corrections for basis set superposition error (BSSE) are investigated by using function counterpoise and its generalized version. It has been found that three‐body terms are attractive in nature and essential in order to describe the cooperative effects in the stable cyclic CO oligomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005