Comment on “ab initio investigation of low-lying 2Σ+ and 2Π states of NO2+”

Energies of the singlet stales of the doubly charged nitric oxide cation have been determined experimentally by the technique of double charge transfer, and are compared with previous results of full-valence MC SCF plus first-order CI techniques. The good agreement obtained permits an assignment of some of the peaks in the experimental spectrum, and confirms the accuracy of these calculations.     

Catalytic reaction mechanism of L-lactate dehydrogenase: an ab initio study

Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion HR- transfer, and the transfers of the hydride ion HR and proton HR are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between the HR transfer process and the hydrogen bonding with lower barrier indicates that the HR transfer process occurs by means of an unusual manner. In addition,     

An ab initio study of the E 3Πg state of the iodine molecule

The E (3)Π(g) state of the iodine molecule is studied by ab initio multireference methods coupled with effective core potentials and large basis sets. Two potential minima are found, a global featuring an ion-pair character, and a local presenting a purely Rydberg nature. Four avoided crossings along the dissociation coordinate attribute an interesting topology to its potential energy curve, and their effect on the vibrational levels of I(2) is discussed.     

Potential energy surfaces for low-lying electronic states of SO_2

The sulfur dioxide molecule (SO2) is an important atmospheric pollutant primarily from sulfur-containing materials combustion processes[1]. Because of its im- portance in atmospheric photochemistry, as well as in atmospheric dynamics, this molecule has been the subject of much experimental[2―10] and theoreti- cal[11―19] photochemical study for many years. They provide a wealth of information about the SO2 spec- trum, predissociation mechanism, vibration including vibration-rotation interact…     

Comment on “ab initio quantum-chemical study of the unimolecular pyrolysis mechanisms of acetic acid”

The mechanisms for dehydration and decarboxylation of acetic acid recently proposed by Ruelle (Chem. Phys. 110 (1986) 263) need to be reexamined because some of the reported transition structures actually correspond to second-order saddle points on the potential energy surface. A new mechanism for the dehydration is suggested involving the intermediacy of 1,1-dihydroxyethylene.     

Reply to comment by farnell and ogilvie on “ab initio calculations of doublet states of NH+”

The effects of perturbation due to the spin-orbit interactions between the X ²Π and a⁴Σ⁻ states on the X-A²Σ⁻ and X-B ²Δ transition moments of NH⁺ are investigated.     

Does the interconversion of polysulfur compounds proceed via hypervalent intermediates? An ab initio MO study

Ab initio MO calculations at the CCSD(T)/6-311++G(2df,p)//MP2/6-311++G** level have been carried out to determine the reaction energies and Gibbs energies of the homolytic dissociation of the S-S bonds in the chainlike sulfanes H2Sn (n = 2-4). Good agreement with the experimental data is observed. At the same level of theory, the formation of the hypothetical sulfuranes H2S(SH)2, H2S(SSH)2, and S(SH)4 from H2S and the mentioned sulfanes has been studied. Species of this type had been proposed as intermediates in the interconversion reactions of polysulfur compounds (e.g., formation of S7 from S8 and vice versa). The three sulfuranes serve here as model compounds. On the basis of the Gibbs energies and activation energies at 298 K, it is shown that the formation of the three sulfuranes from sulfanes requires too much energy and activation energy to successfully compete with homolytic dissociation reactions. In addition, the formation of the methylsubstituted sulfurane S(SMe)4 from the sulfanes Me2S2 and Me2S3 was studied to elucidate the mechanism of the formal exchange of sulfur atoms between polysulfane molecules. However, both the reaction energy of 199 kJ mol(-1) and the activation energy of 287 kJ mol(-1), calculated at the MP2/6-31G* level, are much higher than the homolytic dissociation energy of the S-S bonds in chain- and ringlike polysulfur compounds, such as Me2S4 (140 kJ mol(-1)) and sulfur homocycles (150 kJ mol(-1)). Therefore, it is concluded that the observed interconversion reactions of sulfur rings and of chainlike polysulfanes do not proceed via sulfurane-type intermediates. Instead, these reactions will take place by a radical chain mechanism at high temperatures, while at temperatures below 100 degrees C they are most probably initiated either by traces of nucleophiles that are present as impurities or by the polar surface groups usually present on the walls of the vessels used.     

Role of CH�C�� interaction energy in self-assembled gear-shaped amphiphile molecules: correlated ab initio molecular orbital and density functional theory study

Ab initio molecular orbital and density functional theory calculations with inclusion of dispersion interaction effect are employed to reveal the characteristic features of intermolecular interactions for the molecular capsule (1 ₆) consisting of six gear-shaped amphiphile molecules (1) discovered by Hiraoka et al. (J Am Chem Soc 130:14368?C14369, 2008). The contributions of CH?C?? and ?ШC?? type dispersion energies are found to be indispensable for the formation of hexameric capsule 1 ₆ by the analysis of decomposed interaction energies between fragmented-model species in the 1 molecule. We have also calculated the hexameric capsule (2 ₆) from demethylated 1 molecule (2). Such subtle structural difference induces the different characters of intermolecular interactions, in which the stabilization energy of hexameric 2 ₆ capsule is about 40?kcal/mol smaller than that of the original 1 ₆ capsule, due to the lack of three methyl groups for the CH?C?? interactions in 2 molecules.     

An ab initio Study of Intermolecular Potential for Ne-HBr Complex

ＩｎｔｒｏｄｕｃｔｉｏｎＴｈｅｒａｒｅ ｇａｓｈｙｄｒｏｇｅｎｈａｌｉｄｅ (Ｍ—ＨＸ)ｃｏｍｐｌｅｘｅｓｈａｖｅｌｏｎｇｂｅｅｎｓｔｕｄｉｅｄｆｏｒｉｎｓｉｇｈｔｓｉｎｔｏｔｈｅｎａｔｕｒｅｏｆｉｎ ｔｅｒｍｏｌｅｃｕｌａｒｆｏｒｃｅｓａｎｄｄｅｔａｉｌｓｏｆｉｎｔｅｒ ａｎｄｉｎｔｒａｍｏｌｅｃｕｌａｒｄｙｎａｍｉｃｓ .1,2 ＳｙｓｔｅｍａｔｉｃｉｎｖｅｓｔｉｇａｔｉｏｎｓｏｆｔｈｅｃｏｍｐｌｅｘｅｓｏｆＸｅ ,Ｋｒ,Ａｒ,ａｎｄｌａｔｅｌｙＮｅｗｉｔｈＨＦ ,ＨＣｌ,ＨＢｒａｎｄｔｈｅｉｒｄｅｕｔｅｒａ…     

Adsorption of dimethyl methylphosphonate and trimethyl phosphate on calcium oxide: an ab initio study

Ab initio study of the adsorption of dimethyl methylphosphonate (DMMP) and trimethyl phosphate (TMP) on three types of models simulating the calcium oxide surface (non-hydroxylated Ca₄O₄, completely hydroxylated Ca₄O₄(OH)₂H₂, and partially hydroxylated Ca₄O₄(OH)H) was performed. The target molecule and the surface hydroxyl groups were optimized while the CaO fragment was kept frozen. The intermolecular interactions were investigated applying Bader’s Atoms in Molecules theory. The maps of electrostatic potential of the studied adsorption systems were also produced. The interaction energies of studied adsorption systems corrected by the basis set superposition error were obtained. The most energetically favorable adsorption of DMMP and TMP was found at the configuration where the oxygen atoms of the P=O and methoxy groups point toward the Ca cation of the surface. The P atom points toward the O atom of the surface and forms a P–O chemical bond. This configuration was revealed for the non-hydroxylated and partially hydroxylated CaO-DMMP and CaO-TMP systems. The presence and number of surface hydroxyl groups on the CaO models play a key role in the adsorption of the studied compounds. DMMP and TMP were found to be much less stable on the completely hydroxylated CaO surface where they are adsorbed only via weak electrostatic interactions and H-bonding to the surface oxygen atoms and hydroxyl groups. TMP was found to be slightly more stable on this type of surface than DMMP. The difference in stability is even larger if one compares this TMP system with the complex of tabun adsorbed on completely hydroxylated CaO surface model (Michalkova et al. Chem Phys Lett 438:72, 2007).

Ab initio study of sphere-like mesogen properties

Sphere-like compound C8H17Si(OPhC12H25)3N (1) forms mesophases. In order to investigate the relationship between molecular structure and liquid crystal properties, structural studies are carried out on the model molecules of compound 1 and its substituted derivatives using ah initio calculations. The results show that the cyano or chloro substituted tribenzosilatrane compounds R1Si(OPhR2 )3N (R1 R2 = CN or Cl) have much bigger dipole moments or anisotropy of polarizability and more like sphere than the corresponding alkyl substituted compounds. Cyano or chloro substituted tribenzosilatranes would be better candidates for sphere-like meso-gens.     

Comparative semiempirical and ab initio study of the harmonic vibrational frequencies of aniline—I. The ground state

The harmonic vibrational frequencies of the ground state S₀ of aniline obtained from various ab initio methods [6-31G, 6-31G(*) and 6-31G* basis sets] and semiempirical methods (MINDO/3, MNDO, AM1 and PM3) have been compared to the experimental vibrational spectra. Detailed theoretical analyses of the atomic Cartesian displacements of all normal modes are presented. The semiempirical PM3 method reproduces the experimental frequencies of aniline with comparable accuracy to the ab initio methods. Ale PM3 method will be useful in predicting the vibrational spectra of larger aromatic amines.     

N–H stretching frequencies and the conformation of substituted ureas: an ab initio MO study

The dependence of N–H stretching-mode frequencies in representative di- and trialkyl ureas on the conformational state of the ureido group has been studied by ab initio MO calculations using HF/3-21G and HF/6-31G** basis sets. The molecules studied were 1,3-dimethylurea, 1-methyl-3,3-dimethylurea and 1-methyl-3,3-di-iso-propylurea. The principal conclusions from the ab initio results are:

• 1.the trans–trans conformer (N–H bonds trans to the CO bond) has N–H stretching bands with about 20–30 cm⁻¹ higher frequency than the respective cis–cis structure, in accord with earlier literature assignments based on experimental data;
• 2.the N–H stretching frequency interval in tri-substituted ureas is 15–20 cm⁻¹ higher than the N–H band position in the 1,3-disubstituted molecule studied, the effect being determined mostly by the higher N–H stretching force constant;
• 3.in the absence of the steric hindrance the stable rotameric forms of the ureido grouping are almost planar at HF/3-21G level of calculations, while HF/6-31G** calculations predict a slightly pyramidal structure at the nitrogen atoms in the trans–trans conformer;
• 4.in 1-methyl-3,3-di-iso-propylurea the steric influence of the two bulky iso-propyl groups cause a deviation from planarity of the N–H bond. The non-planar conformation is accompanied by a shift of the N–H stretching mode frequency towards higher values; and
• 5.the variations of the theoretically estimated N–H stretching-mode frequencies appear to be principally determined by changes in the N–H stretching force constants in the different molecules.

© 1997 Elsevier Science B.V.     

Site specificity of OH α-H abstraction reaction for a β-hairpin peptide: an ab initio study

A β-hairpin peptide (PDB ID 1UAO) was modeled to explore the backbone oxidation of a protein by an OH radical to abstract one α-H atom with ab initio calculation at the B3LYB/6-31G(d) without any constraint. Three glycine residues located at three different sites in 1UAO were used to examine the possible site specificity of this backbone oxidation. The pre- and post-reactive complexes along with their associated transition states were located and verified by the intrinsic reaction coordinate method. The reaction profile of these α-H abstraction reactions was constructed. The effects of the aqueous solution were estimated by the conductor-like polarizable continuum model (CPCM) model. Rate constants were calculated with transition state theory. The reaction rate of the OH α-H abstraction varies among these three different sites. The differences among these three sites were rationalized in terms of the molecular and electronic structures of the reactive complexes along the reaction pathway. The explicit solvation effect was estimated through the similar abstraction of a zwitterionic glycine with the combination of microsolvation and a CPCM model. Our results indicate that the α-H abstraction at certain sites requires explicit salvation to obtain accurate results. A replica exchange molecular dynamics simulation was performed to demonstrate the structural change due to this type of abstraction.     

Controlling the strong field fragmentation of ClCHO+ using two laser pulses –an ab initio molecular dynamics simulation

For a single, intense 7 μm linearly polarized laser pulse, we found that the branching ratio for the fragmentation of ClCHO⁺ → Cl + HCO⁺, H + ClCO⁺, HCl⁺+CO depended strongly on the orientation of the molecule (J. Phys. Chem. Lett. 2012 , 3 2541). The present study explores the possibility of controlling the branching ratio for fragmentation by using two independent pulses with different frequencies, alignment and delay. Born-Oppenheimer molecular dynamics simulations in the laser field were carried out with the B3LYP/6-311G(d,p) level of theory using combinations of 3.5, 7 and 10.5 μm sine squared pulses with field strengths of 0.03 au (peak intensity of 3.15×10¹³ W/cm²) and lengths of 560 fs. A 3.5 μm pulse aligned with the C-H bond and a 10.5 μm pulse perpendicular to the C-H bond produced a larger branching ratio for HCl⁺+CO than a comparable single 7 μm pulse. When the 10.5 μm pulse was delayed by one quarter of the pulse envelope, the branching ratio for the high energy product, (HCl⁺+CO 73%) was a factor of three larger than the low energy product (Cl + HCO⁺, 25%). By contrast, when the 3.5 μm pulse was delayed by one quarter of the pulse envelope, the branching ratio was reversed (HCl⁺+CO 38%; Cl + HCO⁺, 60%). Continuous wavelet analysis was used to follow the interaction of the laser with the various vibrational modes as a function of time. © 2018 Wiley Periodicals, Inc.     

A combined experimental inelastic neutron scattering, Raman and ab initio lattice dynamics study of α-lithium amidoborane

A combination of inelastic neutron scattering (INS) spectroscopy and Raman spectroscopy with periodic density functional theory calculations is used to provide a complete assignment of the vibrational spectra of α-lithium amidoborane (α-LiNH(2)BH(3)). The Born charge density and the atomic motion up to the decomposition temperature have been modelled. These models not only explain the nature of bonding in α-LiNH(2)BH(3) but also provide an insight into the atomic mechanisms of its decomposition. The (INS) measurements were performed in the range of 0-4000 cm(-1) on the high-resolution time-of-flight TOSCA INS spectrometer at the ISIS Spallation Neutron Source at the Rutherford Appleton Laboratory.     

Has the trimethylene radical cation been observed?: An Ab initio molecular orbital study

Ab initio calculations have been performed on the cyclopropane radical cation and the trimethylene radical cation. The former radical cation has been claimed to undergo irreversible ring opening to the latter in CFCl₂CF₂Cl matrices at 80 K. However, the computational results reported here show that the energy of the cyclopropane radical cation is much lower than that of the (0,0) trimethylene radical cation, thus casting doubt on the possibility of irreversible ring opening of the former to the latter. It is suggested that the ring-opened species that is observed in the matrix by EPR has a nucleophile strongly coordinated to the carbocationic center.