Minimal basis sets in calculations of intermolecular interaction energies

Several minimal (7, 3/3) Gaussian basis sets have been used to calculate the energies and some other properties of CH₄ and H₂O. Improved basis sets developed for these molecules have been extended to NH₃ and HF and employed to H₂CO and CH₃OH. Interaction energies between XH_n molecules have been calculated using the old and the new minimal basis sets. The results obtained with the new basis sets are comparable in accuracy to those calculated with significantly more extended basis sets involving polarization functions. Binding energies calculated using the counterpoise method are not much different for the new and the old minimal basis sets, and are likely to be more accurate than the results of much more extended calculations.     

A new approach to decoupling of bacterial adhesion energies measured by AFM into specific and nonspecific components

A new method to decoupling of bacterial interactions measured by atomic force microscopy (AFM) into specific and nonspecific components is proposed. The new method is based on computing the areas under the approach and retraction curves. To test the efficacy of the new method, AFM was used to probe the repulsion and adhesion energies present between Listeria monocytogenes cells cultured at five pH values (5, 6, 7, 8, and 9) and silicon nitride (Si₃N₄). Overall adhesion energy was then decoupled into its specific and nonspecific components using the new method as well as using Poisson statistical approach. Poisson statistical method represents the most commonly used approach to decouple bacterial interactions into their components. For all pH conditions investigated, specific energies dominated the adhesion, and a transition in adhesion and repulsion energies for cells cultured at pH 7 was observed. When compared, the differences in the specific and nonspecific energies obtained using Poisson analysis and the new method were on average 2.2 % and 6.7 %, respectively. The relatively close energies obtained using the two approaches demonstrate the efficacy of the new method as an alternative way to decouple adhesion energies into their specific and nonspecific components.     

Classical rotational cross sections for H2—HD and HD—HD collisions

Classical trajectory calculations of integral cross sections for rotationally inelastic collisions of HD-para H₂ and HD—HD were carried out for a wide variety of transitions over a wide range of initial relative translational energies. The results of the HD—H₂ calculations were compared with the quantum effective potential calculations of Chu. It was found that the classical method is in reasonably good agreement with the quantum method for the calculation of rotational transitions of HD at the higher initial translational energies, but the classical method is in poor agreement with quantum results for HD excitation at low energies and for H₂ excitations at all energies.     

Intermolecular interactions of formic acid with benzene: Energy decomposition analyses with ab initio MP2 and double‐hybrid density functional computations

The intermolecular interactions of formic acid (HCOOH) with benzene (C₆H₆) have been investigated using localized molecular orbital energy decomposition analyses (LMO‐EDA) with ab initio MP2 and several double‐hybrid density functionals. The molecular geometries of five HCOOH…C₆H₆ complexes and corresponding benchmark total interaction energies at the CCSD(T)/CBS level are taken from literature (Zhao et al., J. Chem. Theory Comput. 2009, 5, 2726). According to the results of LMO‐EDA with the MP2 method, the dispersion energies are found to be as important as the electrostatic energies for the total interaction energies of the five HCOOH…C₆H₆ complexes. Based on LMO‐EDA with the double‐hybrid density functionals of B2PLYP, B2K‐PLYP, B2T‐PLYP, and B2GP‐PLYP computations, two new parameters for the framework of B2PLYP are extrapolated. These two new parameters are tested with other 10 complexes involving C₆H₆ (Crittenden, J. Phys. Chem. A 2009, 113, 1663), and they perform well on predicting the corresponding total interaction energies. Interestingly, these two new parameters for the framework of B2PLYP also perform well on the noncovalent complexation energies database (NCCE31/05) developed by Truhlar's group (Zhao and Truhlar, J. Phys. Chem. A 2005, 109, 5656). Therefore, these two new parameters appear to be suitable for investigating the noncovalent interactions, and they are denoted as B2N‐PLYP, where N stands for the noncovalent interaction. This study is expected to provide new insight into the derivation of double‐hybrid density functionals for studying the noncovalent interactions. © 2013 Wiley Periodicals, Inc.     

A comparison of Xα LCAO and Xα scattered wave results for A Ni4 cluster

The first results using the Xα LCAO method for a transition metal cluster containing more than two atoms are presented. These results for Ni₄ are compared to those of the Xα scattered wave method and a discussion is given of the Xα orbital energies, Koopman-like orbital energies and Slater transition-state energies for each method.     

An ICSCF investigation of Walsh's rules

The ICSCF method is applied to the calculation of orbital energies as a function of bond angle for several AH₂ molecules. The resulting orbital energy diagrams are quite similar in appearance to the canonical SCF results even though the sum of the ICSCF energies is the SCF energy. The method is also applied to Li₂O, CO₂, HCN and a few AH₃ molecules with similar results. The sum of the ICSCF valence orbital energies generally correlates better with the equilibrium bond angle than does the similar sum of canonical orbital energies.     

Cumulative BK approximation as a method to select configurations for CI calculations of transition energies

A cumulative B_k approximation is examined as a method to select configurations for CI calculations of transition energies where all the matrix elements are computed (full CI). The results obtained by this approach indicate that the transition energies are comparable to the ones obtained at the full CI level. Even for truncation errors of 1 mhartree, the transition energies differ from the full CI ones by less than 0.1 eV.     

Formation of H3+ in Collisions of H2+ with H2 Studied in a Guided Ion Beam Instrument

In order to study collisions between ions and neutrals, a new Guided Ion Beam (GIB) apparatus, called NOVion, has been assembled and tested. The primary purpose of this instrument is to measure absolute cross sections at energies relevant for technical or inter- and circumstellar plasmas. New and improved results are presented for forming H₃⁺ in collisions of H₂⁺ with H₂. Between 0.1 eV and 2 eV, our measured effective cross sections are in good overall agreement with most previous measurements. However, at higher energies, our results do not show the steep decline, recommended in the standard literature. After critical evaluation of all experimental and theoretical data, a new analytical function is proposed, describing properly the dependence of the title reaction on the collision energy up to 10 eV.     

Polarisation potentials for positron-molecule scattering processes

A new form of a local, model polarisation-correlation potential obtained via Density Functional Theory (DFT) is proposed for the treatment of positron scattering from H₂ and N₂ molecules at energies below the threshold of positronium formation. The derivation of the potential is briefly discussed and its relative importance for the elastic channels of the scattering process is analysed in detail. Final elastic cross sections, rotationally summed, are compared with experiments and with existing theoretical results. They are found to agree reasonably well with measurements and suggest the present model as a useful, and simple, method for treating short-range correlation forces in positron scattering calculations for molecular systems.     

Potential energy functions of polyatomic molecules

A direct method is proposed for determining polyatomic potential energy functions, expressed in terms of normal coordinates, which yield a given set of vibrational excitation energies. The method is a modification of the semiclassical technique for computing vibrational energy levels of Percival and Pomphrey. The technique is used to derive potential functions for the NO₂, SO₂ and ClO₂ molecules. With these potentials twenty two higher vibrational excitations energies have been predicted for these molecules and these results differ from the experimental values by at most 3 cm^?1. The computed potential functions are not unique despite the apparent accuracy of the vibrational energy levels. Comparison with the RKR method indicates that the present method must be extended to include rotational perturbations.     

An iterative method for obtaining accurate atomic inner shell binding energies

A new method based on an iterative procedure for obtaining accurate atomic inner shell binding energies is described. The method makes use of the doubly modi-fied Moseley plot as the starting point. As an illustration accurate binding energies for the M ₁ shell in the atomic number range 57 ≤ Z ≤ 71 have been obtained. This has also resulted in the removal of the anomaly in the M ₁ binding energy of Z = 68. Our calculations point to a need for a fresh look at the theoretical calculations of inner shell binding energies for Z = 57 to 71 in which some unsuspected effects appear to occur when the 4f shell is opened, half filled and closed.     

Improved third-order Møller-Plesset perturbation theory

Based on a partitioning of the total correlation energy into contributions from parallel‐ and antiparallel‐spin pairs of electrons, a modified third‐order Møller–Plesset (MP) perturbation theory is developed. The method, termed SCS–MP3 (SCS for spin‐component‐scaled) continues previous work on an improved version of MP2 (S. Grimme, J Chem Phys 2003, 118, 9095). A benchmark set of 32 isogyric reaction energies, 11 atomization energies, and 11 stretched geometries is used to assess to performance of the model in comparison to the standard quantum chemical approaches MP2, MP3, and QCISD(T). It is found, that the new method performs significantly better than usual MP2/MP3 and even outperforms the more costly QCISD method. Opposite to the usual MP series, the SCS third‐order correction uniformly improves the results. Dramatic enhancements are especially observed for the more difficult atomization energies, some of the stretched geometries, and reaction and ionization energies involving transition metal compounds where the method seems to be competitive or even superior to the widely used density functional approaches. Further tests performed for other complex systems (biradicals, C₂₀ isomers, transition states) demonstrate that the SCS–MP3 model yields often results of QCISD(T) accuracy. The uniformity with which the new approach improves for very different correlation problems indicates significant robustness, and suggests it as a valuable quantum chemical method of general use. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1529–1537, 2003     

Multireference perturbation theory with optimized partitioning. II. Applications to molecular systems

The second‐order multireference perturbation theory using an optimized partitioning, denoted as MROPT(2), is applied to calculations of various molecular properties—excitation energies, spectroscopic parameters, and potential energy curves—for five molecules: ethylene, butadiene, benzene, N₂, and O₂. The calculated results are compared with those obtained with second‐ and third‐order multireference perturbation theory using the traditional partitioning techniques. We also give results from computations using the multireference configuration interaction (MRCI) method. The presented results show very close resemblance between the new method and MRCI with renormalized Davidson correction. The accuracy of the new method is good and is comparable to that of second‐order multireference perturbation theory using Møller‐Plesset partitioning. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1390–1400, 2003     

Valence excitation of linear molecules.I. Excitation and UV spectra of N2, Co,acetylene and HCN

Valence excitation energies of N₂, CO, HCCH and HCN are calculated by use of the new quantum-chemical method HAM/3. The average energy thus obtained is then split to give singlet and triplet energies. For ππ* the Recknagel formulas are used. Theoretical and experimental energies are compared. The V-transitions (ππ*¹σ⁺) in CO, HCCH and HCN have been discussed.     

The MT-MSXα(R) method: Applications to Li2, F2, and N2 molecules

The multiple scattering Xα(R) method with the scaling parameter α expressed as a function of the internuclear distance is applied to the Li₂, N₂, and F₂ molecules. Compared with the results obtained by the Xα method, the calculated Xα(R) equilibrium distances are smaller, the total energies are lower, and the dissociation energies are larger.     

Unimolecular neutral and ion kinetics by variable-time neutralization—reionization mass spectrometry

A new method is described for the determination of rate parameters of unimolecular dissociations of neutral intermediates and ions produced by collisional neutralization and reionization at kiloelectronvolt kinetic energies. The method utilizes variable time-scales for neutral and ion dissociations to obtain time-dependent survivor and product ion yields. Kinetic analysis then provides phenomenological rate constants for both neutral and ion dissociations. Neutralization with CH₃I, NO, (C₂H₅)₂O, C₆H₆ and Xe of methyl iodide cation radicals is shown to produce the intermediate neutral molecules with different internal energies, resulting in different rates of neutral and ion dissociations. Vibrational excitation in neutralized CH₃I results in neutral dissociations with rate parameters in the (1–3) × 10⁵ s^–1 range. The origin of neutral excitation by fast collision is explained by the intermediate formation of highly excited Rydberg states that decay by photon emission to the vibrationally excited ground state of the molecule.     

Gas-phase ion-molecule bimolecular and clustering reactions in dilute solutions of acetonitrile in xenon,krypton, argon,neon and helium

Gas-phase bimolecular and clustering reactions of acetonitrile in Xe, Kr, Ar, Ne and He were studied at high chemical ionization pressures in the new coaxial ion source at Auburn. With electron energies near the ionization threshold, the mass spectra are exceedingly simple and are comprised of [CH₄CH]⁺ and clusters of [CH₄CN]⁺ with various ligands such as H₂O and CH₃CN. At higher electron energies many other peaks appear. The intensities of the new peaks depend upon the ionization potential of the charge transfer gas, the ionizing electron energy and the ion source conditions, and are due to reactions of fragment ions. Residence time distributions at electron energies above the ionization threshold (∼ 30 eV) demonstrate that two molecular structures are present in the ion beam at m/z 42, one presumably is protonated acetonitrile ([CH₃CNH]⁺) while the evidence indicates that the second species does not contain acidic hydrogens. With ionizing electron energies near threshold (∼ 10. 5 eV) only one structure is observed. Studies with electron energies near the ionization threshold under high-pressure chemical ionization conditions result in greatly simplified mass spectra and are possible only because of the coaxial geometry of the ion source.     

Theoretical investigation for spectroscopic constants of ground-state alkaline-earth dimers with high accuracy

In this work, we provide highly accurate theoretical estimates for spectroscopic constants of the ground-state alkaline-earth dimers (Ca₂, Sr₂, and Ba₂). Electron correlation energies are calculated with coupled-cluster method at the single, double, and noniterative triple excitations [CCSD(T)] level, and the effects of full triples as well as quadruple excitations are also taken into account at the CCSDT and the CCSDT(Q) level. Our results demonstrate that high-order electron correlation is important to achieve results with high accuracy. We also find that results for Ca₂ with counterpoise corrections, which are designed to eliminate the basis set superposition error, deviate further away from those at the complete basis set limit than the uncorrected ones. The calculated binding energies and equilibrium bond lengths for Ca₂ and Sr₂ are in excellent agreement with recent experimental data. On the other hand, our results for Ba₂ are quite different from previous theoretical data, and there is no available experimental equilibrium bond length and binding energy for calibration. Based on the performance of the adopted approach for Ca₂ and Sr₂, our results should be more reliable and could be helpful for future investigations.