Effects of hydration on scale factors for ab initio force constants

Experimentally measured vibrational frequencies from the polar groups of peptides in aqueous solutions do not agree with frequencies calculated from scaled quantum mechanical force fields (SQMFF) using differential scale factors developed for molecules in the vapor phase. Measured stretching frequencies for carbonyl groups are more than 50 wavenumbers lower than the calculated values. On the other hand, frequencies for non-polar groups calculated using these scale factors are relatively accurate. Our goal is to develop a SQMFF that yields accurate calculated frequencies for peptides in aqueous solutions. To this end, we have calculated scale factors for ab initio force constants for formic acid, acetic acid, and acetone using a least squares fit of calculated and experimental frequencies. We compare these scale factors with changes observed in the ab initio force constants calculated for these molecules at various states of hydration. These force constants are calculated using fully optimized geometries for these hydrated molecules using the 4-31G basis. We present a comparison of the experimental and calculated frequencies, along with their potential energy distributions, for both vapor and aqueous phases. The results indicate that scale factors can simulate the effects of solvation on molecular force constants to yield accurate scaled ab initio force fields.     

Calculating henry adsorption constants of molecular hydrogen at 77 K on alumophosphate zeolites with different microchannel sizes

Adsorption isotherms of molecular hydrogen are measured at 77 K in a series of AlPO alumophosphate zeolites with different microchannel sizes. The potential of the intermolecular interaction of H₂ is calculated within the model of a cylindrical channel of variable size. Henry constants are calculated for this model for arbitrary orientations of the adsorbate molecules in microchannels. The experimental and calculated values of the Henry adsorption constant of H₂ are compared at 77 K on AlPO zeolites. The constants of intermolecular interaction are determined for the H₂-AlPO system.     

Conformational dependence of the n→π* rotatory strength in dissymmetric carboxylic acid compounds

The conformational dependence of the chiroptical properties associated with electronic transitions in α-hydroxy, α-fluoro, α-chloro, and α-mercapto carboxylic acids is examined with a theoretical model in which rotatory strengths are calculated directly from molecular orbitals calculated using INDO and CNDO semi-empirical molecular orbital models, and excited state wave functions constructed in the virtual orbital-configuration interaction approximation. Binding energies, ground state dipole moments, and vertical ionization potentials (calculated according to Koopman's theorem) are calculated, as well as transition energies, dipole strengths, oscillator strengths, rotatory strengths and dissymmetry factors. Special emphasis is placed on correlating the signs of the rotatory strengths calculated for the lowest energy singlet-singlet transitions with conformational isomerism about the C(α)-COOH band of acyclic α-substituted carboxylic acids. The calculated results for S-lactic acid are in agreement with and strongly support the empirically based spectra-structure relationships previously proposed for S-lactic acid and its derivatives. The calculated results for 2(S)-chloropropionic acid do not agree with previously proposed spectra-structure relationships and this finding is discussed. The results obtained for 2(S)-mercaptopropionic acid are in partial agreement with experiment and spectra-structure relationships in this case involve some uncertainty.     

The momentum distribution in some electronic states of the neutral and singly ionized nitrogen molecule

Momentum densities for the N₂ molecule are investigated. Differences between the ground state and low-lying excited states as well as the effects of ionization are discussed. The densities are calculated by taking Fournier transforms of natural spin orbitals of wavefunctions calculated in a minimal basis with configuration interaction.     

Excited state molecular dynamics simulations of nonlinear push–pull chromophores

Julolidinemalononitrile, p-nitroaniline, and julolidinyl-n-N,N^′-diethylthiobarbituric acid are studied with ground and excited state molecular dynamics simulations in conjunction with the collective electronic oscillator formalism and Onsager’s cavity model. Ground and excited state geometries are calculated in the gas phase and four solvents. The results are interpreted in the context of a two-state valence bond model for charge-transfer transitions of conjugated organic molecules, and are compared to recent resonant Raman experimental results. The calculated geometries are qualitatively consistent with both the two-state model and experiment. In addition, calculated transition density matrices are presented to visualize the changes in charge distribution accompanying photoexcitation.     

Features of the fluorine‐substituted acetaldehydes dynamics in the low‐lying electronic states: Quantum mechanical study of the CHF2CHO molecule lowest excited singlet state

The potential energy surface (PES) for the CHF₂CHO molecule in the excited S₁ state is calculated by the CASSCF method. The features of the 1‐ and 2‐D cross‐sections of PES are considered in comparison with those of the relative molecules. The vibrational frequencies are calculated in harmonic approximation and the vibrational energy levels for the inversion motion of the carbonyl fragment CCH_aO and for the torsion motion of the CHF₂‐top are calculated in anharmonic approximation by the 1‐ and 2‐D variational methods. The calculated data are compared with the experimental ones. The problems of the experimental data interpretation are considered. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Methane adsorption on microporous carbon adsorbent with wide pore size distribution

Methane adsorption on a microporous carbon adsorbent with a bimodal pore size distribution is studied at temperatures of 303–333 K at pressures up to 30 MPa. The total micropore volume of the adsorbent, as determined by the Dubinin method, is as large as 1.02 cm³/g. Maximum values of methane adsorption of ≈18 mmol/g are attained at a temperature of 303 K and a pressure of 30 MPa. Methane adsorption isosteres are plotted based on experimental data, and adsorption equilibria at low temperatures are calculated using the linearity of the plots. Experimental isotherms of methane adsorption are compared with the isotherms calculated by the Dubinin–Nikolaev equation with variations in parameters E and n. Temperature dependences of these parameters are determined. Specific characteristics of methane adsorption accumulation are calculated.     

Fluorescence lifetimes and predissociation of the A3Π state of SH+

The high frequency deflection (HFD) technique has been used to obtain fluorescence lifetimes of the SH⁺ A³Π state. The A³Π?X³∑^? electronic transition moment function has been calculated with the complete active space SCF(CASSCF) method. Radiative lifetimes calculated with this transition moment function are compared with measured lifetimes and found to be in good agreement (τ_exp(v′=0)=1.4±0.3 µs; τ_calc=1.6 µs). Deviations between measured and calculated lifetimes forv′=0,J′ ≥ 15 andv′=1,J′=1?7 are interpretated as due to a predissociation caused by a repulsive⁵∑^? state. A simple model, based on a perturbation approach to the predissociation, is used to obtain quantitative estimates of predissociation rates. These calculated rates are in reasonable agreement with the predissociation rates that are inferred from the measured and calculated lifetimes.     

Evaluation of a Combined Quantum Chemical Method Used in Calculating O?H Bond Dissociation Enthalpy

O? H bond dissociation enthalpies (BDE) for a variety of substituted phenols were calculated using a combined quantum chemical method. It is found that the calculated O? H BDE correlated well with the recommended values, except for ortho‐tert‐butyl substituted phenols. For the electron‐donating group substituted phenols the calculated O? H BDE are slightly higher than the recommended values, however, for the electron‐withdrawing group substituted phenols the calculated O? H BDE are slightly lower than the recommended values.     

M1 transition probabilities between fine structure components2L J (L ≥ 1)

Spontaneous emission transition probabilities of the magnetic dipole transitions between states of ground state configurations consisting of onenl electron (or a hole) outside a closed shell have been calculated by using relativistic terms of order α² Z ² and using hydrogenic orbitals to calculate the required overlap integrals. The line strengths calculated for the Boron and Fluorine isoelectronic sequences are in excellent agreement with the calculations involving Dirac wavefunctions for all ions uptoZ=60. The maximum difference at the highest value ofZ=92 is about 6%. Our calculated lifetimes for the state 2p ^{5 2} P _1/2 for Fluorine-like Mg IV and Fe XVIII are 5.03 s and 51.7 µs respectively which are in excellent accord with corresponding values 5.00 s and 51.0 µs calculated by using sophisticated configuration interaction wavefunctions within the Breit-Pauli approximation. Our calculated value of lifetime for Thalium-like Pb II is 40.0 ms which is in good accord with the experimental value of 41.2 ms. New results are presented for the highly ionized ions in the Al-like and Cl-like isoelectronic sequences. The present analysis can be exploited for all the ions in the isoelectronic sequences of elements of groups III A, III B VII A of the periodic table.     

Structural studies on some N-nitramines and N-nitrosamines

INDO-MO calculations are reported for some N-nitramines and N-nitrosamines. Reasonable agreement is obtained between the calculated dipole moments of the lowest energy conformations and experimental data. The calculated energy barrier to rotation about the N-N bond in dimethyl nitrosamine and dimethyl nitramine is in good agreement with experiment. Some calculated spin-spin coupling constants for dimethyl nitramine are also reported.     

Spectroscopic properties of the methyl radical calculated from UHF SCEP wavefunctions

The potential energy surface of symmetric stretching and out-of-plane bending motions for the methyl radical has been calculated from UHF SCEP wavefunctions. Anharmonic vibrational frequencies are computed by a variational method and transition dipole moments and Einstein coefficients of spontaneous emission are reported. Isotropic hyperfine coupling constants are obtained in agreement with experiment to within 4% when calculated by differentiation of the perturbed CEPA-1 energy and taking vibrational averaging into account. Also, the temperature dependence of the proton hyperfine coupling constant compares well with experimental results. The vibrational fine structure of the first band of the photoelectron spectra of CH₃ and CD₃ is calculated in good agreement with experiment.     

Some remarks on the core resonance integral as used in the semi-empirical π-electron calculations

A simple semi-theoretical expression for β, the core resonance integral as used in the semi-empirical π-èlectron calculations has been proposed. β's for some standard C ? C and C ? 0 lengths have been evaluated with the proposed formula and the calculated values are compared with those obtained by other semi-theoretical and empirical methods. Electronic spectra of ethylene, formaldehyde, trans-butadiene and benzene have been calculated by a Pariser-Parr-like semi-empirical method with the values of β thus obtained. The calculated spectra are found to be in good agreement with the observed ones.     

Bond stretching force constants and compressibilities of nitride,oxide, and sulfide coordination polyhedra in molecules and crystals

Molecular quadratic stretching force constants are calculated for a variety of MX bonds (X = N, O, S) in coordinated polyhedra containing row 1 and 2 metal atoms, M, using SCF molecular orbital methods and 6-31G^* basis sets. The resulting data scatter along three distinct trends, depending on whether the bonds involve row 1 atoms, row 1 and row 2 atoms, or row 2 atoms. When compared with spectroscopically determined force constants, the calculated force constants are found to be 20% larger. A single trend seems to obtain when the calculated force constants are plotted as a function of the effective nuclear charges of the bonded atoms and their interatomic separations. Scaled force constants calculated for the SiO bond are in rough agreement with values provided by spectroscopic measurements for silicic acid molecules and silicate crystals. Polyhedral compressibilities for nitride-, oxide-, and sulfide-coordinated polyhedra are inversely related with force constants calculated for their MX bonds. The close similarity of these compressibilities and those recorded for chemically similar crystals suggests that force constant-compressibility relationships in chemically similar molecular and crystalline systems are not significantly different.     

Crystal Structure and Quantum Chemical Ab Initio Calculations of Ibotenic Acid,an Excitatory Amino Acid Receptor Agonist

Ibotenic acid, a constituent of Amanita muscaria, is a potent NMDA receptor agonist. The structure of the ibotenic acid zwitterion monohydrate in the crystalline state has been determined by X-ray crystallography. The crystal structure has two ibotenic acid monohydrate formula units in the asymmetric unit and features an extensive hydrogen bond network. The ibotenic acid zwitter-ions in the crystalline state are compared to the in vacuo structure calculated by quantum chemical ab initio calculations at the HF/6-31+G* level and the effects of the hydrogen bond network on the structures in the solid state are discussed. The calculated potential energy curve with respect to side-chain orientation displays a single energy minimum. The conformations corresponding to the solid-state conformations are calculated to be ca. 2 kcal/mol higher in energy than the minimum-energy conformation in vacuo.     

Semi-empirical calculations of molecular trajectories: Method and applications to some simple molecular systems

The MNDO Hamiltonian as incorporated within MOPAC has been utilized to predict dynamics for some simple reactions. In one option, the intrinsic reaction coordinate has been followed along the path of steepest descent from the transition state backward to reactants and forward to products. In a second option, dynamics of isolated molecular systems have been calculated. In each case, the potential surface (as predicted by the MNDO Hamiltonian) is calculated in situ as the atomic trajectories are calculated from Newton's Laws of Motion. Several specific examples are given and discussed.     

A study of porphin analogues—II: Reactivity indices and spin distribution in some conjugated polyaza macrocycles and their radical ions

Some of the calculated ground state properties of the π-electron system of seven conjugated polyaza macrocyclic ligands are reported, and contrasted with the analogous calculated properties of porphin, tetra-aza porphin and their closed shell dianions.The calculated spin and charge distributions in the anion and cation radicals of the eleven molecules referred to above are also reported in order to assess the perturbation of predicted reactivities by coordination to a central paramagnetic metal ion. The similarity between the Elvidge macrocycle (2) and tetra-aza porphin is particularly noteworthy.     

Critical Micellization Concentration of Ionic Surfactants: Comparison of Theoretical and Experimental Results

Theoretically calculated critical micellization concentration (CMC) of an ionic surfactant and the corresponding experimental value (CMC₀) are compared. The CMC values are calculated within the framework of the quasi-chemical model. The CMC₀ values are determined by the extrapolation of two linear parts of a dependence of a solution property on surfactant overall concentration. These parts of the aforementioned dependences correspond to the premicellar and micellar regions. The difference between CMC and CMC₀ is found to be negligible and comparable with the measurement error. Cases in which this difference must be taken into account when estimating the properties of micellar solutions are discussed. It is shown that the micellization constant K _c of surfactant molecules can be calculated from the data on CMC₀.     

Theoretical study on the mechanism and kinetics of addition of hydroxyl radicals to fluorobenzene

Geometries, frequencies, reaction barriers, and reaction rates were calculated for the addition of OH radical to fluorobenzene using Möller–Plesset second‐order perturbation (MP2) and G3 methods. Four stationary points were found along each reaction path: reactants, prereaction complex, transition state, and product. A potential for association of OH radical and fluorobenzene into prereaction complex was calculated, and the associated transition state was determined for the first time. G3 calculations give higher reaction barriers than MP2, but also a significantly deeper prereaction complex minimum. The rate constants, calculated with Rice–Ramsperger–Kassel–Marcus (RRKM) theory using G3 energies, are much faster and in much better agreement with the experiment than those calculated with MP2 method, as the deeper well favors the formation of prereaction complex and also increases the final relative populations of adducts. The discrepancies between the experimental and calculated rate constants are attributed to the errors in calculated frequencies as well as to the overestimated G3 reaction barriers and underestimated prereaction complex well depth. It was possible to rectify those errors and to reproduce the experimental reaction rates in the temperature range 230–310 K by treating the relative translation of OH radical and fluorobenzene as a two‐dimensional particle‐in‐the‐box approximation and by downshifting the prereaction complex well and reaction barriers by 0.7 kcal mol^?1. The isomeric distribution of fluorohydroxycyclohexadienyl radicals is calculated from the reaction rates to be 30.9% ortho, 22.6% meta, 38.4% para, and 8.3% ipso. These results are in agreement with experiment that also shows dominance of ortho and para channels. © 2012 Wiley Periodicals, Inc.     

Direct dynamics study on the mechanism and the kinetics of the reaction of CH3NH2 with OH

A theoretical study of the mechanism and the kinetics for the hydrogen abstraction reaction of methylamine by OH radical has been presented at the CCSD(T)/6‐311 ++G(2d,2p)//CCSD/6‐31G(d) level of theory. Our theoretical calculations suggest a stepwise mechanism involving the formation of a prereactant complex in the entrance channel and a preproduct complex in the exit channel, for the two hydrogen abstraction channels involving the methyl and amine groups. For clarity, the diagram of potential for the reaction is given. The calculated standard reaction enthalpies are ?98.48 and ?76.50 kJ mol^?1 and barrier heights are 0.36 and 25.25 kJ mol^?1, respectively. The rate constants are evaluated by means of the improved canonical variational transition state theory with small‐curvature tunneling correction (ICVT/SCT) in the temperature range of 299–3000 K. The calculated results show that the rate constants at experimentally measured temperatures are in good agreement with the experimental values. It is shown that the calculated rate constants exhibit a non‐Arrhenius behavior. Moreover, the variational effect is obvious in the calculated temperature range. The dominant product channel is to form CH₂NH₂ and H₂O via hydrogen abstraction from the CH₃ group of CH₃NH₂ by OH in the calculated temperature range. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009