Response to: “Comment on ‘The effect of confinement on the electronic energy and polarizability of a hydrogen molecular ion’”

In this reply we clarify questions point out in the Comment on: “The Effect of Confinement on the Electronic Energy and Polarizability of a Hydrogen Molecular Ion” by J. F. da Silva, F. R. Silva and E. Drigo Filho, Int. J. Quantum Chem.2016, 116, 497–503 written by S. A. Cruz and H. Olivares‐Pilón. In particular, we show how we made the calculations of ground state energy from the confined hydrogen molecule ion for cavities of different volumes. The internuclear distances to the excited state 2pσ_u are also presented.     

The effect of confinement on the electronic energy and polarizability of a hydrogen molecular ion

The electronic energy and the polarizability of a confined hydrogen molecular ion in the ground state and the first excited state, for cavities of different volumes, are calculated using the variational method. In the treatment adopted an alternative molecular wave function is introduced with only one variational parameter and based on wave functions used for confined atoms. © 2016 Wiley Periodicals, Inc.     

Calculation of quasiparticle energy of molecular systems by the GW method

The quasiparticle energy of the H₂ molecule is calculated by using the GW method, in which the self‐energy operator fully depends on the frequency. The initial Green function G₀ is constructed from the wave function obtained by the Hartree–Fock approximation (HFA) and local density approximation (LDA) in the framework of the density functional theory (DFT). From the results obtained we have shown that the wave function from the DFT–LDA is more effective than that from the HFA for G₀. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem 84: 348–353, 2001     

Comment on “The effect of confinement on the electronic energy and polarizability of a hydrogen molecular ion” by Josimar Fernando da Silva,Fabricio Ramos Silva and Elso Drigo Filho,Int. J. Quantum Chem. 2016, 116, 497–503

Various conceptual and numerical errors reported in the paper cited in the title of this contribution are pointed out and clarified. Our main concern is the evident violation of the variational principle, which is used in that paper for the study of the confined hydrogen molecular ion to obtain both energies and properties.     

Variational problem for ground and excited rovibronic states on the basis of a molecular Hamiltonian in the principal central axes

A general scheme of realization of nonempirical methods for calculation of the ground and excited rovibronic states of flexible molecules is proposed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Simplest proof of the Jahn–Teller theorem for molecular systems

A new simple proof of the Jahn–Teller theorem for molecular systems is presented. The proof is based on some general properties of symmetric square representation characters that simplify their explicit treatment and minimize the use of tables. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Explicitly correlated variational estimates of the energy levels of negative hydrogen ion under spatial confinement

Comprehensive investigations on the structural modifications of negative hydrogen ion within an impenetrable spherical domain has been performed in the framework of Ritz variational method. Electron correlation plays a major role in the formation of H^– ion. The Hylleraas‐type basis set expansion of wave function considered here incorporates the effect of electron correlation in an explicit manner. Energy values of and 1sn states of H^– ion within confined domain have been calculated. Although the singly excited states do not exist for a “free” H^– ion, well converged energy values of such states have been found within a wide range of confinement radius. The thermodynamic pressure felt by the ion inside the sphere is also estimated. The general trend shows successive destabilization of the excited energy levels with increase of pressure. The contribution of angular correlation in the energy values have been estimated. Evolution of and energy levels of H^– ion as quasi‐bound states are being reported.     

Assessment and acceleration of binding energy calculations for protein–ligand complexes by the fragment molecular orbital method

In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics‐based force fields, although they cannot fully describe protein–ligand interactions. A noteworthy computational method in development involves large‐scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large‐scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange‐correlation functionals, and solvation effects) on the binding energies of the FK506‐binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2‐MP2/6‐31G(d), is suitable for evaluating the protein–ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure–activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein–ligand interaction distance. Our acceleration scheme, which uses FMO2‐HF/STO‐3G:MP2/6‐31G(d) at R_int = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy. © 2015 Wiley Periodicals, Inc.     

The VMFCI method: a flexible tool for solving the molecular vibration problem

The present article introduces a general variational scheme to find approximate solutions of the spectral problem for the molecular vibration Hamiltonian. It is called the "vibrational mean field configuration interaction" (VMFCI) method, and consists in performing vibrational configuration interactions (VCI) for selected modes in the mean field of the others. The same partition of modes can be iterated until self-consistency, generalizing the vibrational self-consistent field (VSCF) method. As in contracted-mode methods, a hierarchy of partitions can be built to ultimately contract all the modes together. So, the VMFCI method extends the traditional variational approaches and can be included in existing vibrational codes based on the latter approaches. The flexibility and efficiency of this new method are demonstrated on several molecules of atmospheric interest.     

Formulation of Strutinsky's method for atomic systems in the extended Kohn–Sham scheme

Strutinsky's standard averaging method is formulated in the framework of the extended Kohn–Sham scheme and a two‐step procedure permitting the application of the method is proposed. A Taylor‐series expansion of the ground‐state energy‐function of the occupation numbers is derived, which involves the averaged energy as the leading term and shell corrections as smaller terms. Numerical applications for atoms and ions from Be through Ar are presented and discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

The maximum hardness and minimum polarizability principles as the basis for the study of reaction profiles

New and useful aspects of chemical reactivity as described by reactivity indexes and used in connection with the maximum hardness and minimum polarizability principles (MHP and MPP, respectively) are discussed and illustrated for two classical reactions in organic chemistry. They include the Beckmann rearrangement and the condensation reactions of -amino acids. The MPP appears as a more general rule than the MHP. Another relevant result is related to the usefulness of both empirical reactivity rules to predict the most probable reaction mechanism among two different pathways displaying very close values in activation energy (competitive pathways). This is illustrated for the condensation reaction of a series of -amino acids: while the accepted stepwise route follows both the MHP and MPP rules, the alternative concerted channel does not, yet its associated activation energy is slightly lower than that corresponding to the nonconcerted reaction mechanism.From the Proceedings of the 28th Congresco de Quimicos Teóricos de Expresión Latina (QUITEL 2002)     

Mild method for the synthesis of 1H-indazoles through oxime-phosphonium ion intermediate

The synthesis of 1H-indazoles from o-aminobenzoximes is achieved via N–N bond formation using triphenylphosphine, I₂, and imidazole. Selective formation of oxime-phosphonium ion intermediate in the presence of the amino group is the driving force for this reaction. The nucleophilicity of the arylamino group and electrophilicity toward the N–O bond of oxime also control the reaction. The reaction proceeds at a faster rate with good to excellent yield under this mild reaction condition and is amenable to scale-up.     

Calculations of molecular polarizabilities using the Valence Effective Hamiltonian (VEH) method

In this paper, we investigate the applicability of the Valence Effective Hamiltonian (VEH) method to calculations of theoretical molecular linear polarizabilities by the Sum-Over-States (SOS) methodology. Test calculations are presented on the polyene series. They indicate that the method gives qualitatively the same trends asab initio small basis sets calculations.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

Stereoselective synthesis of an advanced taxusin intermediate: an application of the type 2 intramolecular Diels–Alder reaction

Stereoselective synthesis of an advanced taxusin intermediate is described. The key step is the successful application of the type 2 intramolecular Diels–Alder (IMDA) reaction for the assembly of the tricyclic core of this natural product.     

Current‐density functional study of the HeH+ molecular ion under a strong ultrashort magnetic field

The HeH⁺ molecular ion under an ultrashort magnetic field on the order of 10⁹ G is investigated through quantum fluid dynamics and a current‐density functional theory (CDFT) based approach, employing a vector exchange–correlation (XC) potential which depends on the electronic charge‐density as well as on the current‐density. The behavior of the exchange and correlation energies of the HeH⁺ ion is analyzed and compared with those obtained using an approach based on the time‐dependent density functional theory (TD‐DFT) under similar computational constraints but employing a scalar XC potential dependent only on the electronic charge‐density. The CDFT‐based approach yields exchange and correlation energies as well as TD electronic charge‐densities drastically different from those obtained using the TD‐DFT‐based approach particularly, at typical TD magnetic field strengths. This is attributed to the nonadiabatic effects induced by the vector XC potential of the CDFT in the oscillating charge‐density of the HeH⁺ ion, which are further explained in the terminology of quantum fluid dynamics. The vector XC potential of the CDFT‐based approach is observed to augment the magnetic interactions in the H₂ molecule and in the He ion, whereas it opposes the magnetic interactions in the HeH⁺ ion particularly, at the intermediate magnetic field strengths. © 2012 Wiley Periodicals, Inc.     

Dynamic changing features of the molecular face for interaction of a rare gas atom with a hydrogen molecule

We perform a systematical investigation on the dynamic changing feature of the molecular shape and size and electron density distribution in the process of a rare‐gas atom (He, Ne, Ar, and Kr) approaching a hydrogen molecule by an ab initio method. In terms of the molecular face (MF) theory, the polarization effect in the above processes is vividly demonstrated. There is a good linear correlation between our average variation rate (S_aver) of molecular intrinsic characteristic radius at the contacting point and the experimental polarizability of the rare‐gas atoms. This indicates that the MF theory can well represent the intermolecular polarization effect. Interestingly, the pictures of shape changing, charge‐flow, and exchange repulsion processes especially on the reacting active areas have been clearly observed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Optimization and validation of an ion‐pair RP‐HPLC‐UV method for the determination of total free iodine in rabbit plasma: application to a pharmacokinetic study

An ion‐pair reverse‐phase high performance liquid chromatographic method with UV–vis detection has been developed for the determination of total free iodine in rabbit plasma after vaginal administration of povidone–iodine (PVP‐I). Sample preparation was done by protein precipitation with acetonitrile in 96‐well format and aspirin was used as the internal standard. The 100 µL sodium thiosulfate solution (5 g L^?1) was added to 100 µL plasma sample before protein precipitation, to convert the total free iodine in plasma to iodide (I^?). Separation was performed on a C₁₈ column (200 × 4.6 mm i.d., 5 µm). The mobile phase consisting of a mixture of water phase (containing 10 mmol L^?1 18‐crown‐6 ether, 5 mmol L^?1 octylamine and 5 mmol L^?1 sodium dihydrogen phosphate, pH adjusted to 6.0 with phosphoric acid) and acetonitrile in the ratio 70:30 (v/v) was delivered isocraticly at a flow rate of 1.0 mL min^?1. The method was sensitive with a lower limit of quantification of 0.005 µg mL^?1, with good linearity (r² > 0.9990) over the linear range of 0.005–2 µg mL^?1. All the validation data, such as linearity, accuracy and precision, were within the required limits. The method was successfully applied to study the pharmacokinetic of PVP–I in rabbits after vaginal administration. Copyright © 2009 John Wiley & Sons, Ltd.     

On the calculation of arbitrary multielectron molecular integrals over Slater‐type orbitals using recurrence relations for overlap integrals. II. Two‐center expansion method

Using expansion formulas for the charge‐density over Slater‐type orbitals (STOs) obtained by the one of authors [I. I. Guseinov, J Mol Struct (Theochem) 1997, 417, 117] the multicenter molecular integrals with an arbitrary multielectron operator are expressed in terms of the overlap integrals with the same screening parameters of STOs and the basic multielectron two‐center Coulomb or hybrid integrals with the same operator. In the special case of two‐electron electron‐repulsion operator appearing in the Hartree–Fock–Roothaan (HFR) equations for molecules the new auxiliary functions are introduced by means of which basic two‐center Coulomb and hybrid integrals are expressed. Using recurrence relations for auxiliary functions the multicenter electron‐repulsion integrals are calculated for extremely large quantum numbers. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 117–125, 2001