The intermolecular interaction in the charge-transfer complexes between amines and halogens: A theoretical characterization of the trends in halogen bonding

The trends in the properties of prereactive or charge-transfer complexes formed between the simple amines NH₃, CH₃NH₂, (CH₃)₂NH, and (CH₃)₃N and the halogens F₂, ClF, Cl₂, BrF, BrCl, and Br₂ were investigated by the ab initio restricted Hartree–Fock approach, the Møller–Plesset second-order method, and with several density functional theory variants using extended polarized basis sets. The most important structural parameters, the stabilization energies, the dipole moments, and other quantities characterizing the intermolecular halogen bond in these complexes are monitored, discussed, and compared. A wide range of interaction strengths is spanned in these series. Successive methyl substitution of the amine as well as increasing polarities and polarizabilities of the halogen molecules both systematically enhance the signature of charge-transfer interaction. These trends in halogen bonds of varying strength, in many aspects, parallel the features of hydrogen bonding.     

Accurate and efficient determination of higher roots in diagonalization of large matrices based in function restricted optimization algorithms

The problem of large‐scale matrix diagonalization is analyzed in the context of normal function optimization techniques with particular emphasis on the problem of obtaining high roots. New methods based on function restricted optimization algorithms are presented. The efficiency of these methods is illustrated for lowest and higher and degenerate roots of selected matrices. The diagonalization process is commonly carried out in a subspace, and involves a sort of optimization process, and the dimension of this subspace increases at each iteration. In addition, the success of a diagonalization method in obtaining a desired root strongly depends on the particular optimization procedure chosen. In this work, a rational function optimization procedure is presented that permits obtaining the lowest and higher eigenpairs in an efficient way. Update Hessian matrices formulae, routinely used in normal function optimization problems, are explored in the framework of diagonalization techniques. Finally, a diagonalization method with a fixed subspace dimension during the iterative process is presented. Some examples focused in lowest, higher and degenerate eigenpairs are discussed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1375–1386, 2000     

Determination of serum cortisol using isotope dilution–liquid chromatography–mass spectrometry as a candidate reference method

We propose isotope-dilution mass spectrometry as a candidate reference method for determination of serum cortisol. The method uses liquid chromatography–mass spectrometry (LC–MS), interfaced with electrospray ionization, and selective monitoring of the [M+H]⁺ ions of cortisol and isotopically labeled cortisol. The isotope-dilution–liquid chromatography–mass spectrometry (ID–LC–MS) method simplifies sample-preparation, because samples are processed by simple solvent extraction without further clean-up and derivatization. We studied the time required for complete equilibration of endogenous cortisol and labeled cortisol spiked into serum and found it to be less than 1 h. The repeatability and the reproducibility of the method were evaluated and found to be 0.55% of the measurement value. CRM 192 and 193 from the Bureau Communautaire de Reference were analyzed for verification of the method. The results obtained from the ID–LC–MS method agreed with the certified values. The relative uncertainty of measurement results for samples in the range of a few tens of micrograms per kilogram to several hundred micrograms per kilogram was evaluated and found to be 0.56%. Immunoassay carried out by three independent clinical laboratories produced results more than 15% higher than this ID–LC–MS method, suggesting the presence of bias in the immunoassay methods.     

Using the UPLC–ESI–Q‐TOF–MSE method and intestinal bacteria for metabolite identification in the nonpolysaccharide fraction from Bletilla striata

Bletilla striata (Thunb.) Reichb. f. (Orchidaceae), also known as Bai‐ji, is a traditional Chinese herb that is widely used in Asia to treat hematemesis, hemoptysis, traumatic bleeding and other similar disorders. Most studies have focused on the pharmacological activities of polysaccharide extracts from B. striata. Our previous studies found that the nonpolysaccharide fraction from B. striata extract also has a hemostatic effect; however, the active constituents responsible for this pharmacological action are unclear. Thus, the metabolic profiles of the nonpolysaccharide fraction were investigated in Sprague–Dawley rats and intestinal bacteria models using ultra‐performance liquid chromatography coupled with quadrupole time‐of‐flight tandem mass spectrometry. Mass data were acquired by the MS^E method. Eight components including five prototypes and three metabolites were identified in rat biofluids after oral administration of the nonpolysaccharide fraction. The parent compounds underwent various metabolic processes, including hydrolysis, deglucosylation, glycosylation and sulfate conjugation. The results not only reveal the possible metabolic pathway, but also indicate the potential pharmacological components. Further mechanistic studies using nonpolysaccharide compounds of the B. striata extract are required to obtain potential candidate compounds.     

Ab initio and density functional studies on the structure and vibrational spectra of 2-hydroxy-1,4-naphthoquinone-1-oxime derivatives

Structure and vibrational frequencies of lawsoneoxime and its C₃-substituted (R=CH₃, NH₂, Cl, NO₂) derivatives in keto and nitrosophenol forms have been obtained employing the Hartree–Fock and density functional methods. Charge distributions in different conformers have been studied using the molecular electrostatic potential topography as a tool. For all these derivatives except for nitrolawsoneoxime the amphi conformer in the keto form is predicted to be of lowest energy, which can partly be attributed to hydrogen bonding through the oximino nitrogen. In the nitro derivative, however, the preference to form a six membered ring owing to O–H–O hydrogen-bonded interactions makes the anti conformer (keto) the stablest. Further one of the nitrosophenol conformers of nitrolawsoneoxime turns out to be very close in energy (0.21 kJ mol^–1 higher) to this anti conformer. The consequences of hydrogen bonding on charge distribution and vibrational spectra are discussed.     

The ground state of TiC revisited

The ground state of TiC is ³⁺, as predicted by previous configuration interaction calculations. It is shown that there are two low-lying ¹⁺ states and that the density functional theory solution corresponds to the higher of the two ¹⁺ states.Contribution to the Björn Roos Honorary Issue     

Ab initio study of C4H3 potential energy surface and reaction of ground‐state carbon atom with propargyl radical

The potential energy surface for the reaction of the ground‐state carbon atom [C(³P_j)] with the propargyl radical [HCCCH₂(X²B₁)] is investigated using the G2M(RCC,MP2) method. Numerous local minima and transition states for various isomerization and dissociation pathways of doublet C₄H₃ are studied. The results show that C(³P_j) attacks the π system of the propargyl radical at the acetylenic carbon atom and yields the n‐C₄H₃(²A′) isomer i3 after an 1,2‐H atom shift. This intermediate either splits a hydrogen atom and produces singlet diacetylene, [HCCCCH ( p1 )+H] or undergoes (to a minor amount) a 1,2‐H migration to i‐C₄H₃(²A′) i5 , which in turn dissociates to p1 plus an H atom. Alternatively, atomic carbon adds to the triple C?C bond of the propargyl radical to form a three‐member ring C₄H₃ isomer i1 , which ring opens to i3 . Diacetylene is concluded to be a nearly exclusive product of the C(³P_j)+HCCCH₂ reaction. At the internal energy of 10.0 kcal/mol above the reactant level, Rice–Ramsperger–Kassel–Marcus calculations show about 91.7% of HCCCCH comes from fragmentation of i3 and 8.3% from i5 . The other possible minor channels are identified as HCCCC+H₂ and C₂H+HCCH. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1522–1535, 2001     

A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Prostaglandin H synthase catalyzes the oxygenation of arachidonic acid into the cyclic endoperoxide, prostaglandin G₂ (PGG₂), and the subsequent reduction of PGG₂ to the corresponding alcohol, prostaglandin H₂ (PGH₂), the precursor of all prostaglandins and thromboxanes. Both radical abstraction by a neighboring tyrosyl radical and combined radical/carbocationic models have been proposed to explain the cyclooxygenase part of this reaction. We have used density functional theory calculations to study the mechanism of the formation of the cyclooxygenated product PGG₂. We found an activation free energy for the initial hydrogen abstraction by the tyrosine radical of 15.6 kcal/mol, and of 14.5 kcal/mol for peroxo bridge formation, in remarkable agreement with the experimental value of 15.0 kcal/mol. Subsequent steps of the radical-based mechanism were found to happen with smaller barriers. A combined radical/carbocation mechanism proceeding through a sigmatropic hydrogen shift was ruled out, owing to its much larger activation free energy of 36.5 kcal/mol. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0476-9. Electronic Supplementary MaterialSupplementary material is available in the online version of this article at Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

LC–ESI–MS/MS determination of copanlisib,a novel PI3K inhibitor,in mouse plasma and its application to a pharmacokinetic study in mice

A sensitive, selective and rapid LC–ESI–MS/MS method has been developed and validated for the quantification of copanlisib in mouse plasma using enasidenib as an internal standard (IS) as per regulatory guideline. Copanlisib and the IS were extracted from mouse plasma using ethyl acetate as an extraction solvent and chromatographed using an isocratic mobile phase (0.2% formic acid–acetonitrile; 25:75, v/v) on a HyPURITY C₁₈ column. Copanlisib and the IS eluted at ~0.95 and 2.00 min, respectively. The MS/MS ion transitions monitored were m/z 481.1 → 360.1 and m/z 474.0 → 456.0 for copanlisib and the IS, respectively. The calibration range was 3.59–3588 ng/mL. The intra‐ and inter‐batch accuracy and precision (RE and RSD) across quality controls met the acceptance criteria. Stability studies showed that copanlisib was stable in mouse plasma for one month. This novel method has been applied to a pharmacokinetic study in mice.     

Depurated inversion method for orbital‐specific exchange potentials

This work presents exchange potentials for specific orbitals calculated by inverting Hartree–Fock wavefunctions. This was achieved by using a Depurated Inversion Method. The basic idea of the method relies on the substitution of Hartree–Fock orbitals and eigenvalues into the Kohn–Sham equation. Through inversion, the corresponding effective potentials were obtained. Further treatment of the inverted potential should be carried on. The depuration is a careful optimization which eliminates the poles and also ensures the fullfilment of the appropriate boundary conditions. The procedure developed here is not restricted to the ground state or to a nodeless orbital and is applicable to all kinds of atoms. As an example, exchange potentials for noble gases and term‐dependent orbitals of the lower configuration of Nitrogen are calculated. The method allows to reproduce the input energies and wavefunctions with a remarkable degree of accuracy.     

Exact solution of Schrödinger equation with deformed ring-shaped potential

Exact solution of the Schrödinger equation with deformed ring-shaped potential is obtained in the parabolic and spherical coordinates. The Nikiforov–Uvarov method is used in the solution. Eigenfunctions and corresponding energy eigenvalues are calculated analytically. The agreement of our results is good.AMS Subject Classification: 03.65.–w, 12.39.Jh, 21.10.–k     

Bond length alternation in ground and HOMO→LUMO excited states in polyenes. Dynamic Stokes shift?

Complete-active-space self-consistent-field calculation of the reorganisation energy, , corresponding to the strongly allowed HOMOLUMO transition in planar polyenes in the trans form (C _{2 h} symmetry), gives >0.5 eV. This large depends on the fact that the short and long bond lengths of the excited ¹B _u (or ³B _u ) state compared to the ¹A _g ground state are almost cancelled. The emission redshift (Stokes shift) in molecules with the same type of system is quite small, however, which suggests that the Stokes shift may be dynamic, owing to the presence of another excited state at lower or about the same energy. Acknowledgement.We congratulate Björn on his birthday and at the same time thank him for the CASSCF method and for many years of collaboration and help from him and his collaborators to make this wonderful method work in our laboratory.Contribution to the Björn Roos Honorary Issue     

Formulation of unrestricted and restricted Hartree–Fock–Bogoliubov equations

The Hartree–Fock–Bogoliubov (HFB) method, dealing with Bogoliubov orbitals, which consist of particle and hole part, can provide states with pair correlations associated with Cooper pairs. The dimension of HFB Fock matrices can be reduced by restrictions of spin states of Bogoliubov orbitals similarly to ordinary Hartree–Fock (HF) equations such as restricted HF (RHF), unrestricted HF (UHF), and generalized HF (GHF). However, there are few studies of moderate restricted HFB equations such as UHF‐based HFB equations. In this article, formulation and calculations of restricted HFB equations are described. The solutions of general and restricted HFB equations are compared. Pair correlations taking account of restricted and general HFB equations are discussed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Application of the field‐theoretic method of Bohm and Pines to a study of the metal–insulator transition in doped dielectric media

A treatment based on the field‐theoretic formalism of Bohm and Pines is presented which reproduces theoretically the essential features of the Mott–Edwards–Sienko relation, na∼¼, for the location of the metal–insulator transition in doped dielectric media, where n_c is the critical electron concentration and a is the effective radius. The model allows a study to be made of the dopant electronic wave function from the localized insulating state through to the metallic regime. The effective interparticle interaction shows Friedel oscillations and, at short range, is close to the Thomas–Fermi form. The doping dependence of the electronic hyperfine interaction, total dielectric constant, and ionization energy for a disordered collection of s‐state one‐electron atoms in a structureless dielectric medium are derived and both are found to be in satisfactory qualitative agreement with experiment. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 111–120, 1999     

Effect of nitrogen on mechanical,oxidation and structural behaviour of Ti–Si–B–C–N nanocomposite hard coatings deposited by DC sputtering

Ti–Si–B–C–N film was deposited by DC magnetron sputtering at different argon and nitrogen ratios such as N₂/Ar = 1 : 5, 2 : 4, 3 : 3, 4 : 1 and 5 : 0. The formation of TiN and TiB phases was observed because of incorporation of nitrogen. The hardness, modulus, microstructure, structure and bond formation with different nitrogen contents during the deposition were studied by nanoindentation, scanning electron microscope, X‐ray diffraction and X‐ray photoelectron spectroscopy, respectively. The oxidation kinetics of Ti–Si–B–C–N was investigated. The nitrogen incorporation during deposition influences different properties of the coating. Hardness and modulus decreased, and microstructure showed very fine grain presence, and film changes to fully amorphous because of incorporation of nitrogen in the film. Copyright © 2016 John Wiley & Sons, Ltd.     

New structural parameters of fullerenes for principal component analysis

The Kekulé structure count and the permanent of the adjacency matrix of fullerenes are related to structural parameters involving the presence of contiguous pentagons p, q, r, q/p and r/p, where p is the number of edges common to two pentagons, q is the number of vertices common to three pentagons and r is the number of pairs of nonadjacent pentagons adjacent to another common pentagon. The cluster analysis of the structural parameters allows classification these parameters. Principal component analysis (PCA) of the structural parameters and the cluster analyses of the fullerenes permit their classification. PCA clearly distinguishes five classes of fullerenes. The cluster analysis of fullerenes is in agreement with PCA classification. Cluster analysis shows greatest similarity for the q–q/p and r–r/p pairs. PCA provides five orthogonal factors F ₁–F ₅. The use of F ₁ gives an error of 28%. The inclusion of F ₂ decreases the error to 2%.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002)     

The performance of density functional theory for LnF (Ln=Nd,Eu, Gd,Yb) and YbH

Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue     

Systematic convergence of energies with respect to basis set and treatment of electron correlation: focal-point conformational analysis of methanol

A practical means of overcoming the limitation in accuracy of conformational analysis due to incompleteness of basis sets used in ab initio calculations involves calculating the energy with a series of systematically improving basis sets and extrapolating to the basis set limit. We report here a focal-point conformational analysis for methanol. The Hartree–Fock energy converges exponentially to the basis set limit, while the convergence of second-order correlation energy is well described by the formula . This formula also describes well the convergence of fourth-order correlation energy. The height of the rotational barrier at the Hartree–Fock level can be obtained reliably by taking the difference of the extrapolated energies of the two conformations and correcting the difference for correlation effects. Electron correlation has only a small decreasing effect on the height of the rotational barrier in methanol. The focal-point value for the torsional barrier in methanol is 0.999±0.007 kcal/mol. Acknowledgement.This project was supported by Provost Funds at University of California, Santa Barbara (UCSB). The computational resources were provided partially by the National Computational Science Alliance and UCSBs Supercomputer Facility. We also acknowledge the Horgan Award (University of Missouri-Columbia) to K. K., which made possible the purchase of additional computational resources. We thank Robert Gdanitz and Bernie Kirtman for valuable discussions and Jozef Noga for providing us with a copy of the DIRCCR12-OS program.     

Modeling water exchange on monomeric and dimeric Mn centers

Water exchange on Mn centers in proteins has been modeled with density functional theory using the B3LYP functional. The reaction barrier for dissociative water exchange on [Mn^IV(H₂O)₂(OH)₄] is only 9.6 kcal mol^–1, corresponding to a rate of 6×10⁵ s^–1. It has also been investigated how modifications of the model complex change the exchange rate. Three cases of water exchange on Mn dimers have been modeled. The reaction barrier for dissociative exchange of a terminal water ligand on [(H₂O)₂(OH)₂Mn^IV(-O)₂Mn^IV(H₂O)₂(OH)₂] is 8.6 kcal mol^–1, while the bridging oxo group exchange with a ring-opening mechanism has a barrier of 19.2 kcal mol^–1. These results are intended for interpretations of measurements of water exchange for the oxygen evolving complex of photosystem II. Finally, a tautomerization mechanism for exchange of a terminal oxyl radical has been modeled for the synthetic O₂ catalyst [(terpy)(H₂O)Mn^IV(-O)₂Mn^IV(O)(terpy)]³⁺ (terpy=2,2:6,2-terpyridine). The calculated reaction barrier is 14.7 kcal mol^–1.Contribution to the Björn Roos Honorary Issue