Initio Study Research Articles

An ab initio quantum chemical study of reaction mechanisms in the C2H2/CH3OH/KOH/DMSO system

An ab initio quantum chemical study (MP2/6-311++G**//B3LYP/6-31+G*) of a number of possible interactions is performed for the gas phase system of acetylene—potassium hydroxide-dimethylsulfoxide(DMSO)—methanol and with regard to the solvent effect within the continuum model. Key structures in the vinylation reaction are shown to be methoxide ion complexes with the alkali metal hydroxide and acetylene molecules. The formation of these complexes results in the activation of the acetylene molecule and an increase in the nucleophilicity of the methoxide ion. In the C2H2/CH3OH/KOH/DMSO reaction system, a proton exchange between the acetylene molecule and the anionic nucleophile ([OH]- and [CH3O]-) is freely performed with the formation of systems with ethynideions, whereas the thermodynamically preferable formation of vinyl alcohol or methyl vinyl ether is determined by a barrier of 20 kcal/mol.

Structures and Vibrational Spectra of the Hydrogen-Bonded Complexes Between Nitrous Acid and Acetone: Ab Initio and DFT Studies

ABSTRACT The structures, stability, and vibrational spectra of the binary complexes formed between acetone and nitrous (trans and cis) acid have been investigated using ab initio calculations at the SCF and MP2 levels and B3LYP calculations with 6-311++G(d,p) basis set. Full geometry optimization was made for the complexes studied. It was established that the complex (CH3)2CO···HONO-trans is more stable than the complex (CH3)2CO···HONO-cis by 0.5–0.8 kcal·mol−1. The accuracy of the calculations has been estimated by comparison between the predicted values of the vibrational characteristics (vibrational frequencies and infrared intensities) and the available experimental data. It was established, that the methods, used in this study are well adapted to the problem under examination. The predicted values with the B3LYP/6-311++G(d,p) calculations are very near to the results, obtained with MP2/6-311++G(d,p). The calculated frequency shift Δν(O‒H) for the complex (CH3)2CO···HONO-trans (1A) is larger than for the complex (CH3)2CO···HONO-cis (1B). In the same time the intensity of this vibration increases dramatically upon hydrogen bonding. The calculated increase for the complex 1A is up to 15 times and for the complex 1B is up to 30 times. The changes in the vibrational characteristics (vibrational frequencies and infrared intensities) of (CH3)2CO upon the complexation are more insignificant than the changes in the vibrational characteristics of HONO-trans and HONO-cis.

N′,N′-dialkylhydrazides and their protonated forms: ab initio calculations and studies by physical methods

RHF/6-31G(d) and MP2/6-31G(d) quantum-chemical calculations of N′,N′-dimethylethanohydrazide molecule and also MP2/6-31G(d) calculations of its protonated forms were performed. With the use of IR and 1H NMR spectroscopy the series of N′,N′-dialkylhydrazides and their salts with HCl and H2SO4 were studied. The position of proton addition was determined. The experimental results were compared with the calculated findings.

Soft-phonon instability in zincblende HgSe and HgTe under moderate pressure:Ab initiopseudopotential calculations

The mercury chalcogenides HgSe and HgTe show peculiar behavior under moderate compression such as the unusual observation of a ``hidden'' transition from their ambient-pressure zincblende phase to an orthorhombic metastable phase with space group $C{222}_{1}$. We present here the results of an ab initio pseudopotential study within the framework of the density-functional theory of the stability of the low-pressure zincblende phases of HgSe and HgTe and the transition to the $\text{C}{222}_{1}$ structure. We relate the observation of the $\text{C}{222}_{1}$ phase to an instability in the transverse-acoustic phonon branches of the zincblende phases of these materials. We have studied in detail the mechanism of the $\text{zincblende}\ensuremath{\rightarrow}\text{C}{222}_{1}$ transition as well as the structural evolution of the $\text{C}{222}_{1}$ phase under pressure.

Calculation of the charge transfer transition energy of the mesitylene–ICl complex by ab initio and TDDFT methods: Comparison with other methylbenzene–ICl complexes

Of the four plausible isomeric structures of the mesitylene–ICl charge transfer (CT) complex, the most feasible one was determined by a detailed ab initio and DFT study at the HF, B3LYP and MPW1PW91 levels using the 6-31++G(d,p) basis set. Potential energy surface scans followed by frequency calculation and full optimization revealed that the I–Cl bond, with its I atom oriented towards the aromatic ring, stands vertically above an unsubstituted C-atom, being inclined at about 6° to the C 3-axis. Complexation increases the I–Cl bond length. Correction for basis set superposition error through a counterpoise calculation yields a binding energy close to the experimental value. The electronic CT transition energy (hν CT) with this ground-state structure as input was calculated in vacuo by the CIS method and in carbon tetrachloride medium by the TDDFT method under the polarizable continuum model. In a similar way the values of hν CT were calculated for complexes of ICl with p-xylene, durene and hexamethylbenzene. Throughout the series of methylbenzene complexes, the TDDFT-calculated values of hν CT were less than the experimental values and such underestimation may be attributed to the inherent difficulties of DFT to take into account long-range interactions. However, the trend of the variation of hν CT with the number and position of methyl groups in the series was reasonably similar to the trend followed by the experimental CT transition energies.

Optical spectra of bismuth sulfochloride crystals

We present the results of the ab initio theoretical study of the optical properties for paraelectric BiSCl crystal using the full potential linearized augmented plane wave (FP-LAPW) method as implanted in the Wien 2k code. For theoretical calculations of optical constants and functions we used the generalized gradient approximation (PBE-GGA), an improvement of the local spin-density approximation (LSDA) and recently Wu–Cohen (WC) proposed a new WC-GGA exchange-correlation energy functional. The dielectric function, refractive index, extinction coefficient, absorption coefficient, reflectivity, and energy loss function were calculated. The optical properties are analyzed and the origins of the peaks in the spectra are discussed in terms of the calculated density of states.

Ab initio pseudopotential study of vacancies and self-interstitials in hcp titanium

By means of an ab initio plane-wave pseudopotential method, monovacancy, divacancy and self-interstitials in hcp titanium are investigated. The calculated monovacancy formation energy is 1.97 eV, which is in excellent agreement with other theoretical calculations, and agrees qualitatively with published experimental results. The relaxation of the atoms around a single vacancy is observed to be small. Two divacancy configurations, the in-plane and the off-plane, have also been shown to be equally stable. With regards to the interstitials, of the eight configurations studied, two (octahedral and basal octahedral) have relatively lower formation energies and are, thus, the most likely stable configurations. We find small energy differences between them, suggesting their possible co-existence. It is also observed that the tetrahedral configuration decays to a split dumbbell configuration, whereas both the basal tetrahedral and the basal pseudocrowdion interstitials decay to the basal octahedral configuration. Using the nudged elastic band method (NEB), we determine a possible minimum energy path (MEP) for the diffusion of self-interstitial titanium atoms from an octahedral site to the nearest octahedral site. The energy barrier for this migration mechanism is shown to be about 0.20 eV.

Ab initio structural parameters and transition pressures of GaN x As1− x dilute alloys

The results are presented of an ab initio total energy study of the high-pressure phases of GaN x As1− x dilute alloys calculated within the full-potential linearized augmented plane wave method in the generalized gradient approximation. Three candidate structures, namely zinc-blende, rocksalt and CsCl, have been considered. In each case, the structural parameters and transition pressures of dilute alloys of interest are calculated. In agreement with earlier calculations of Stenuit and Fahy [Phys. Rev. B 76 (2007) 035201], the deviation of the lattice constants from Vegard's law for zinc-blende GaN x As1− x alloys is found to be negligible.

Ab initio supermolecule study of charge transfer in the glyoxal-formamide and in the H2S-formamide systems

Ab initio supermolecule calculations have been performed for the glyoxal–formamide and for the H2S–formamide charge transfer complexes in their ground states. According to the results obtained with Mulliken's population analysis, glyoxal acts always as an electron acceptor against formamide which we have used as model compound for a peptide group. The results indicate also that the amount of transferred charge depends strongly on the intermolecular distance and on the relative orientation of the molecular planes. On the other hand we have found that H2S against our expectation acts at most relative geometrical positions as an electron acceptor with respect to formamidc.

Quantum-mechanical studies of environmental effects on biomolecules. III. Ab initio model studies of the hydration of peptides and proteins

Ab initio SCF calculations on the hydration of the peptide linkage and of the hydrophilic amino acid side chains of proteins are used to evaluate the binding energies and the most likely positions of the water molecules of the first hydration shell. The results are compared with the very scarce available experimental data.

Direct ab initio molecular dynamics study of F atom reaction with methane

The dynamics of the F + CH4 → HF + CH3 and F + CD4 → DF + CD3 reactions have been investigated using classical trajectory calculations at the MP2/cc-pvdz level of theory. The trajectories were calculated directly from electronic structure computations, and a Hessian based method with updating was used to integrate the trajectories. Using this method, product rovibrational populations and internal energy distributions were obtained for the F + CH4 and F + CD4 reactions. The theoretical results were compared with the available experimental data and previous calculations results. The state distributions of the reaction F + CH4 in these calculations are in reasonable agreement with the experimental results, which indicates that the experimental behavior of the reaction could be well reproduced by the direct classical trajectory calculations at MP2/cc-pvdz level. As such, the product rovibrational populations and internal energy distributions for the reaction F + CD4 were predicted. The same degree of agreement between theory and experiment as the F + CH4 reaction is expected.

Extraction and ab initio calculation studies on the complexation of Ca2+ with valinomycin

From extraction experiments and γ-activity measurements, the exchange extraction constant corresponding to the equilibrium Ca2+ (aq)+1·Sr2+ (nb) ⇆ 1·Ca2+ (nb) + Sr2+ (aq) taking place in the two-phase water-nitrobenzene system (1 = valinomycin; aq = aqueous phase, nb = nitrobenzene phase) was evaluated as log Kex (Ca2+, 1·Sr2+) = 2.4±0.1. Further, the stability constant of the valinomycin-calcium complex (abbrev. 1·Ca2+) in nitrobenzene saturated with water was calculated for a temperature of 25 °C: log βnb (1·Ca2+) = 8.3±0.1. By using quantum mechanical DFT calculations, the most probable structure of the 1·Ca2+·2H2O complex species was predicted. In this complex, the “central” Ca2+ cation is bound by strong bonds to two oxygen atoms of the respective water molecules and to four ester carbonyl oxygens of the parent valinomycin ligand 1. Finally, the calculated binding energy of the considered complex 1·Ca2+·2H2O is −319.2 kcal/mol, which confirms the relatively high stability of this cationic complex species.

Ab initio and DFT theory studies of interaction of thymine with formaldehyde

In this article, the interaction of formaldehyde (FA) with thymine is theoretically investigated by computational chemistry methods. The optimization geometries and vibrational frequencies of FA, thymine and three complexes between thymine and FA have been calculated by using the density functional theory and ab initio methods at the B3LYP/6-311G(d, p) and MP2/6-311G(d, p) levels. The NBO and AIM methods are used to analyse interaction as well. Conformers (A), (B) and (C) are cyclic structures with C–H***O and N–H***O hydrogen bonds on a common plane. The corrected complex interaction energies of cyclic structures (A), (B) and (C) at MP2/6-311G(d, p) levels are −38.41, −26.94 and −26.01 kJ/mol, respectively. The order of stability is (A) > (B) > (C).

Electronic Selection Rules Controlling Dislocation Glide in bcc Metals

The validity of the structure-property relationships governing the low-temperature deformation behavior of many bcc metals was brought into question with recent ab initio density functional studies of isolated screw dislocations in Mo and Ta. These relationships were semiclassical in nature, having grown from atomistic investigations of the deformation properties of the group V and VI transition metals. We find that the correct form for these structure-property relationships is fully quantum mechanical, involving the coupling of electronic states with the strain field at the core of long a/<2111> screw dislocations.

The effect of electron correlation on the conformational space of melatonin

The pineal gland hormone melatonin regulates several physiological processes including circadian rhythm and also alleviates oxidative stress-induced degenerative diseases. In spite of its important biological roles, no high level ab initio conformational study has been conducted to reveal its structural features. In this work, the conformational flexibility of melatonin was investigated using correlated ab initio calculations. Conformers, obtained previously at the Hartree-Fock level (HF/6-31G*), were fully optimized using second order Møller-Plesset perturbation theory applying the frozen core approximation (MP2(FC)/6-31G*). Furthermore, single-point MP4(SDQ,FC)/6-31G*//MP2(FC)/6-31G* computations were performed to investigate the effect of higher order perturbation terms. The HF and MP2 conformational spaces are considerably different: the initial 128 structures converged into 102 different local minima as confirmed by frequency calculations; 28 new minima appeared and 26 previous HF local minima disappeared; no "all-trans" C3 side chain conformations are seen at the MP2(FC) level. The MP2 global minimum conformation is stabilized by an aromatic-side chain interaction.

Health-Related Quality of Life Outcomes in HIV-Infected Patients Starting Different Combination Regimens in a Randomized Multinational Trial: The INITIO-QoL Substudy

The health-related quality of life (HRQoL) outcomes in HIV-infected, treatment-naive patients starting different HAART regimens in a 3-year, randomized, multinational trial were compared. HRQoL was measured in a subgroup of patients enrolled in the INITIO study (153/911), using a modified version of the MOS-HIV questionnaire. The regimens compared in the INITIO trial were composed by two NRTIs (didanosine + stavudine) plus either an NNRTI (efavirenz) or a PI (nelfinavir), or both (efavirenz + nelfinavir). Primary HRQoL outcomes were Physical and Mental Health Summary scores (PHS and MHS, respectively). During follow-up, an increase of PHS score was observed in all treatment arms. The MHS score remained substantially unchanged with the four-drug combination and showed with both NNRTI- and PI-based three-drug regimens a marked trend toward improvement, which became statistically significant when a multiple imputation method was used to adjust for missing data. Overall, starting all the combination regimens compared in the INITIO study was associated with a maintained or slightly improved HRQOL status, consistently with the positive immunological and virological changes observed in the main study. The observed differences in the MHS indicate a possible HRQoL benefit associated to the use of three-drug, two-class regimens and no additional benefit for the use of four-drug, three-class regimens, confirming that three-drug, two-class regimens that include two NRTIs plus either an NNRTI or a PI should be preferred as initial treatment of HIV infection.

An ab initio quantum-chemical study of C6H5SO2CH3 and C6H5SO2CF3 in the MP2(full)/6-31+G* approximation with NBO analysis of wave functions

Potential functions of internal rotation around $$C_{sp^2 } - S$$ bonds in C6H5SO2Ch3 (I) and C6H5SO2CF3 (II) were obtained by ab initio MP2(full)/6-31+G* calculations. The revealed stationary points were identified by solving vibration problems. In the energetically favorable conformations of I and II, the $$C_{sp^2 } - S - C_{sp^3 } $$ plane is perpendicular to the benzene ring plane. The barriers to rotation around the $$C_{sp^2 } - S$$ bonds in I and II are 20.81 and 28.23 kJ mol−1, respectively. The parameters of the molecular geometry were estimated. The wave functions were analyzed using the NBO formalism, and the distribution of natural charges over atoms was considered.

Ab initio and DFT study of the inner mechanism and dynamic stereochemistry of electrophilic addition reaction of bromine to bisbenzotetracyclo[6.2.2.23,6.02,7]tetradeca-4,9,11,13-tetraene

The inner mechanism and dynamic stereochemistry of electrophilic addition of bromine to bisbenzotetracyclo[6.2.2.2(3,6).0(2,7)]tetradeca-4,9,11,13-tetraene(BBTT) molecule have been investigated by the methods of quantum chemistry. The structure of the BBTT molecule has been studied by ab initio and DFT/B3LYP methods using the 6-31G(d) and 6-311G(d) basis sets. The double bonds of BBTT molecule are endo-pyramidalized. The structure and stability of the cationic intermediates and products of the addition reaction have been investigated by HF/6-311G(d), HF/6-311G(d,p), B3LYP/6-311G(d) and B3LYP/6-311++G(2d,p)//B3LYP/6-311G(d) methods. The bridged bromonium cation isomerized into the more stable nonclassical delocalized N- and U-type cations and the difference between the stability of these cations is small. For the determination of the direction of addition reaction and the stereochemistry of the products, the stability of nonclassical delocalized N- and U-type ions and the structure of their cationic centres play a vital role. Since the cationic centre of the N-type ion is in interaction with the benzene ring from the exo face, the nucleofilic attackof the bromide anion to this centre occurs from the endo face and the exo,endo-isomer of the N-type product is obtained. The attack of bromide anion, towards the cationic centre of U-type ion from the endo face is sterically hindered by the hydrogen atom therefore the attack occurs from the exo face, which interacts with the benzene ring and the more stable exo,exo-isomer of U-type product is formed. Although, the U-type cation was 2.232 kcal mol(-1) more stable than the N-type cation, the U-type product was 0.587 kcal mol(-1) less stable than the N-type product.

On some hydrogen bond correlations at high pressures

Structural data from in situ high pressure neutron diffractions studies are analysed to show that the measured lengths of O‒H and H---O pairs in hydrogen bonds follow the correlation between them established from 0.1 MPa data on different chemical compounds. In particular, the accepted view in literature that the high pressure data on ice VIII differ from it is not supported. For compounds in which the O‒H stretching frequencies red shift under pressure, it is shown that wherever structural data is available, they follow the stretching frequency versus H---O (or O---O) distance correlation. For compounds displaying blue shifts with pressure, an analogy appears to exist with ‘improper’ hydrogen bonds. Another pressure effect expected is the symmetrization of a hydrogen bond with evolution of the double-welled, hydrogen bond potential into a single-well potential. Using the results from some recent ab initio electronic structure studies, we show that the bulk modulus shows a discontinuity at this point and this can be taken as signature for hydrogen bond symmetrization. This is supported by analysing a few available experimental data.

Ab initio quantum-chemical study of the reaction mechanisms of acetylene in superbasic media. Noncatalytic vinylation of methanol

The reaction profile of noncatalytic vinylation of methanol with acetylene was studied by ab initio quantum-chemical calculations for the gas phase and by calculations using a combined model that took into account the solvent (DMSO) effect. The reaction occurs via the formation of a prereaction complex of the methoxide ion with acetylene; at this stage, the acetylene molecule is already activated with respect to the proton. The observed stereospecific trans-addition in methanol vinylation in the gas phase and solution is provided by the lower activation barrier corresponding to the E structure of the acetylene molecule in the transition state and barrier-free protonation of the carbanion intermediate.