The MC‐DFT approach including the SCS‐MP2 energies to the new minnesota‐type functionals

We have applied the multicoefficient density functional theory (MC‐DFT) to four recent Minnesota functionals, including M06‐2X, M08‐HX, M11, and MN12‐SX on the performance of thermochemical kinetics. The results indicated that the accuracy can be improved significantly using more than one basis set. We further included the SCS‐MP2 energies into MC‐DFT, and the resulting mean unsigned errors (MUEs) decreased by approximately 0.3 kcal/mol for the most accurate basis set combinations. The M06‐2X functional with the simple [6–311+G(d,p)/6–311+G(2d,2p)] combination gave the best performance/cost ratios for the MC‐DFT and MC‐SCS‐MP2|MC‐DFT methods with MUE of 1.58 and 1.22 kcal/mol, respectively. © 2014 Wiley Periodicals, Inc.     

Mechanism for the gas‐phase reaction between OH and 3‐methylfuran: A theoretical study

The mechanism for the OH + 3‐methylfuran reaction has been studied via ab initio calculations to investigate various reaction pathways on the doublet potential energy surface. Optimizations of the reactants, products, intermediates, and transition structures are conducted using the MP2 level of theory with the 6‐311G(d,p) basis set. The single‐point electronic energy of each optimized geometry is refined with G3MP2 and G3MP2B3 calculations. The theoretical study suggests that the OH + 3‐methylfuran reaction is dominated by the formation of HC(O)CH?C(CH₃)CHOH (P7) and CH(OH)CH?C(CH₃)C(O)H (P9), formed from two low‐lying adducts, IM1 and IM2. The direct hydrogen abstraction pathways and the S_N2 reaction may play a minor or negligible role in the overall reaction of OH with 3‐methylfuran. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical Comparison of the Linear and Bent Structures for the Weakly Bound CO2—HF Complex

Density‐functional theory method (DFT) B3LYP/6–311++G(3df,2pd) and Moller‐Plesset perturbation method (MP2) MP2/6–311++G(3df,2pd) of Gaussian 03 were selected for the theoretical study of weakly bound CO₂—HF complex. In addition to the well‐known linear structure, the various bent structure complexes were also found in this work. The self‐consistent energy differences were only around 0.02 kJ/mol between the bent structure and linear structure by comparison. From the results of H‐bonding distance, dHF elongation and red shift of VHF vibration frequency, all the evidence shows that the H‐bonding effect in the bent structure is stronger than the linear structure. However, if one compares the Gibbs energy of the complex formation by temperature variation, it is very easily found that the linear form is favored under the thermal conditions of most temperatures whenever T ≥ 40 K. Such a fact is consistent with the former spectroscopic observed result of Klemperer et al.     

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.     

An experimental and computational approach to pH‐dependent self‐aggregation of poly(2‐isopropyl‐2‐oxazoline)

Besides temperature, self‐aggregation of poly(2‐isopropyl‐2‐oxazoline) (PIPOX) can also be triggered via pH in aqueous solution (25 °C, pH > 5). Lowest energy structures and interaction energies of PIPOX with H₃O⁺, OH^?, and H₂O were calculated by DFT methods showed that, in addition to their ability to protonate PIPOX, H₃O⁺ ions had strong interaction with both water and PIPOX in acidic conditions. H₃O⁺ ions acted as compatibilizer between PIPOX and water and increased the solubility of PIPOX. OH^? ions were found to have stronger interaction with water compared to PIPOX resulting in desorption of water molecules from PIPOX phase and decreased solubility, leading to enhanced hydrophobic interactions among isopropyl groups of PIPOX and formation of aggregates at high pH. Results concerning the effect of end‐groups on aggregate size were in good agreement with statistical mechanics calculations. Moreover, the effect of polymer concentration on the aggregate size was examined. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 210–221     

Computational Study of the Dissolution of Some Atomic and Diatomic Species in the Square and Hexagonal 2‐D Helium Lattices

Dissolution of some industrially relevant atomic and diatomic species (Ar, Ne, H, O, H₂, N₂ and O₂) in the 5 × 5 2‐D hexagonal and square helium lattices, as the model of the liquid helium cryogen, has been studied using ab initio MP2/6‐31++G computations. Structural, electronic and thermochemical properties have been calculated and analyzed for these solution lattices. Results of these calculations show that dissolution of Ar, Ne, H and H₂ species is more favored at higher temperatures. A reverse trend is observed for the dissolution of O, N₂ and O₂ species. A staggered orientation is preferred by all diatomic species in both lattices. Results of this study also show that breakage of the O₂ molecule becomes slightly easier in the 2‐D helium lattices as compared with that of the H₂ molecule. Effect of the cavity geometry and size, and position of the solute in the lattice have also been studied. Analysis of the results shows that the range of the interaction between the solute and solvent atoms is only one helium layer.     

DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR

The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational properties. As a demonstration of its applicability to biomacromolecular systems, the method, referred to as DIRECT‐ID, was used to identify relevant ligand‐modulated structural variations in the β₂‐adrenergic (β₂AR) G‐protein coupled receptor. Micro‐second MD simulations of the β₂AR in an explicit lipid bilayer were run in the apo state and complexed with the ligands: BI‐167107 (agonist), epinephrine (agonist), salbutamol (long‐acting partial agonist), or carazolol (inverse agonist). Each ligand modulated the conformational dynamics of β₂AR differently and DIRECT‐ID analysis of the inverse‐agonist vs. agonist‐modulated β₂AR identified residues known through previous studies to selectively propagate deactivation/activation information, along with some previously unidentified ligand‐specific microswitches across the GPCR. This study demonstrates the utility of DIRECT‐ID to rapidly extract functionally relevant conformational dynamics information from extended MD simulations of large and complex macromolecular systems. © 2015 Wiley Periodicals, Inc.     

Carbondioxide rare‐gas systems: Sensitivity of basis sets and double‐hybrid density functionals

This study emphasizes on the performance of six newly developed double‐hybrid density functionals (DHDF) in explaining the potential energy curves of different carbondioxide rare‐gas systems. The basis set sensitivity has also been explored with the use of three basis sets. Our results suggest that for lighter He/Ne‐CO₂ complexes, proper choice of DHDF and basis set lead to results those matches exactly with earlier calculations and also with the experiment. On the other hand, for heavier Ar/Kr‐CO₂ complexes although the equilibrium separation distance matches exactly with earlier observations, the interaction energy values lie far apart. The overall investigation emphasizes on the fact that one has to tune the methods and basis sets properly to achieve good and satisfactory results. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

亚烷基锡烯与乙烯环加成反应机理的理论研究

The mechanism of a cycloaddition reaction between singlet alkylidenestannylene and ethylene has been investigated with MP2/3-21 G^* and B3LYP/3-21 G* methods, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies for the involved conformations were calculated by CCSD(T)//MP2/3-2 IG^* and CCSD(T)//B3LYP/3-21G^* methods, respectively. The results show that the dominant reaction pathway of the cycloaddition is that an intermediate (INT) is firstly formed between the two reactants through a barrier-free exothermic reaction of 39.7 kJ/mol, and the intermediate then isomerizes to a four-membered ring product (P2.1) via a transition state TS2.1 with a barrier of 66.8 kJ/mol.     

Reply to A Computational Evaluation of the Evidence for the Synthesis of 1,3‐Dimethylcyclobutadiene in Solid State and Aqueous Solution—Beyond the Experimental Reality

Following earlier reports on the photochemical synthesis of 1,3‐dimethylcyclobutadiene 8 , 10 in a protective host matrix, theoretical calculations for the formation of that adduct have been recently performed by Rzepa. 13 The author formulated criticisms based mainly on density functional theory calculations of ¹H NMR spectra. According to Rzepa the calculated spectra do not correspond with our measured spectra, which leads him to the conclusion that our interpretation is wrong, and that mainly cyclobutadiene has not been stabilized or even synthesized; we believe, however, that the initial model that Rzepa used for his calculations does not correspond to chemical reality or is at the very least a crude simplification of it, which implies that his calculations cannot match, in every point, our experimental spectra. Rzepa′s simplified models might be ‘reasonable’ from the theoretical point of view; however, in the case of assessment in the solid state, the theoretical setup does not force the system to preserve the confined stabilizing space defined by the crystalline matrix for encapsulated hosts in the solid state. Inversely, in the case of solution modeling, the theoretical setup is too rigid to properly assess the complex equilibria occurring in solution and to accurately determine the NMR spectra of exchanging species in solution. The inconsistency between our experimental results and the results of the theoretical models proposed by Rzepa is such that his conclusions are considered to be too far from experimental reality. Accurate modeling taking in account “reasonable” experimental details would be a worthwhile endeavor.     

Simultaneous determination of niacin and its metabolites—nicotinamide,nicotinuric acid and N‐methyl‐2‐pyridone‐5‐carboxamide—in human plasma by LC‐MS/MS and its application to a human pharmacokinetic study

An LC‐MS/MS method for the simultaneous quantitation of niacin (NA) and its metabolites, i.e. nicotinamide (NAM), nicotinuric acid (NUA) and N‐methyl‐2‐pyridone‐5‐carboxamide (2‐Pyr), in human plasma (1 mL) was developed and validated using nevirapine as an internal standard (IS). Extraction of the NA and its metabolites along with the IS from human plasma was accomplished using a simple liquid–liquid extraction. The chromatographic separation of NA, NAM, NUA, 2‐Pyr and IS was achieved on a Hypersil‐BDS column (150 ¥ 4.6 mm, 5 mm) column using a mobile phase consisting of 0.1% formic acid : acetonitrile (20:80 v/v) at a flow rate of 1 mL/min. The total run time of analysis was 2 min and elution of NA, NAM, NUA, 2‐Pyr and IS occurred at 1.37, 1.46, 1.40, 1.06 and 1.27 min, respectively. A detailed validation of the method was performed as per the FDA guidelines and the standard curves were found to be linear in the range of 100–20000 ng/mL for NA; 10–1600 ng/mL for NUA and NAM and 50–5000 ng/mL for 2‐Pyr with mean correlation coefficient of ≥0.99 for each analyte. The method was sensitive, specific, precise, accurate and suitable for bioequivalence and pharmacokinetic studies. The developed assay method was successfully applied to a pharmacokinetic study in humans. Copyright © 2010 John Wiley & Sons, Ltd.     

Theoretical influence of third molecule on reaction channels of weakly bound complex CO2… HF systems

In this investigation, reaction channels of weakly bound complexes CO₂…HF, CO₂…HF…NH₃, CO₂…HF…H₂O and CO₂…HF…CH₃OH systems were established at the B3LYP/6‐311++G(3df,2pd) level, using the Gaussian 98 program. The conformers of syn‐fluoroformic acid or syn‐fluoroformic acid plus a third molecule (NH₃, H₂O, or CH₃OH) were found to be more stable than the conformers of the related anti‐fluoroformic acid or anti‐fluoroformic acid plus a third molecule (NH₃, H₂O, or CH₃OH). However, the weakly bound complexes were found to be more stable than either the related syn‐ and anti‐type fluoroformic acid or the acid plus third molecule (NH₃, H₂O, or CH₃OH) conformers. They decomposed into CO₂ + HF, CO₂ + NH₄F, CO₂ + H₃OF or CO₂ + (CH₃)OH₂F combined molecular systems. The weakly bound complexes have four reaction channels, each of which includes weakly bound complexes and related systems. Moreover, each reaction channel includes two transition state structures. The transition state between the weakly bound complex and anti‐fluoroformic acid type structure (T₁₃) is significantly larger than that of internal rotation (T₂₃) between the syn‐ and anti‐FCO₂H (or FCO₂H…NH₃, FCO₂H…H₂O, or FCO₂H…CH₃OH) structures. However, adding the third molecule NH₃, H₂O, or CH₃OH can significantly reduce the activation energy of T₁₃. The catalytic strengths of the third molecules are predicted to follow the order H₂O < NH₃ < CH₃OH. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Theoretical study of two C50H40 isomers with three dodecahedrane cages sharing two pentagons

Structures, energies, and vibrational frequencies have been calculated for two C₅₀H₄₀ isomers with three dodecahedrane cages sharing two pentagons at the B3LYP/6‐31G* level of theory. Thus, two C₅₀H₄₀ isomers have the form of coplanar tri‐dodecahedrane‐cage molecules. The symmetry of one isomer is D_5d and that of another is C_2V. Heats of formation and vertical ionization energies for two C₅₀H₄₀ isomers have been estimated in this study. Heats of formation as well as vibrational analysis indicate that two C₅₀H₄₀ isomers enjoy sufficient stability to allow for its experimental preparation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Insights into the mechanism of methionine oxidation catalyzed by metal (Cu2+, Zn2+, and Fe3+)—Amyloid beta (Aβ) peptide complexes: A computational study

In this DFT study, a mechanism of the oxidation of methionine (Met) amino acid residue catalyzed by the metal (Cu²⁺, Zn²⁺, and Fe³⁺) bound amyloid beta (Aβ) peptide has been proposed. Based on experimental information, two different mechanisms: (1) stepwise and (2) concerted mechanisms for this important process have been investigated. The B3LYP calculations suggest that in the stepwise mechanism, the two separate pathways leading to the same sulfoxide product [Met(O)] go through prohibitively high barriers of 27.3 and 35.1 kcal/mol, therefore it is ruled out. In the concerted mechanism, the Cu²⁺‐Aβ complex has been found to be the most efficient catalyst with the computed barrier of 14.3 kcal/mol. The substitutions of Cu²⁺ by Zn²⁺ and Fe³⁺ increase barriers to 19.6 and 16.9 kcal/mol, respectively and make the reaction thermodynamically less favorable. It was also found that, in comparison with the cysteine (Cys) residue, Met is more susceptible toward oxidation. Its substitution with Cys slightly increased the barrier to 15.8 kcal/mol for the Cu²⁺‐Aβ complex. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

A density‐functional theory approach to the separation of K2ZrF6 and K2HfF6 via fractional crystallization

Because of the low absorption cross‐section for thermal neutrons of zirconium (Zr) as opposed to hafnium (Hf), Zr‐metal must essentially be Hf‐free (<100 ppm Hf) to be suitable for use in nuclear reactors. However, Zr and Hf always occur together in nature, and due to very similar chemical and physical properties, their separation is particularly difficult. Separation can be achieved by traditional liquid–liquid extraction or extractive distillation processes, using Zr(Hf)Cl₄ as feedstock. However, the production of K₂Zr(Hf)F₆ via the plasma dissociation route, developed by the South African Nuclear Energy Corporation Limited (Necsa), could facilitate the development of an alternative separation process. In this theoretical study, the results of density‐functional theory (DFT) simulations of K₂Zr_(1‐z)Hf_zF₆ solid solutions [using Cambridge Serial Total Energy Package (CASTEP)] are presented, for which the supercell approach was applied in an attempt to determine whether solid solution formation during crystallization from aqueous solutions (fractional crystallization) is thermodynamically possible, which would hinder the separation efficiency of this method. Consequently, the calculated thermodynamic properties of mixing were used to evaluate the separation efficiency of Zr and Hf by fractional crystallization using a thermodynamic model to calculate the relative distribution coefficients. The small mixing enthalpies that were calculated from the DFT results, indicates that lattice substitution of Zr(IV) by Hf(IV) in K₂ZrF₆ could occur with relative ease. This is not surprising, considering the close similarities between Zr and Hf, and it was therefore concluded that K₂Zr_(1‐z)Hf_zF₆ solid solution formation might well restrict the separation efficiency of Zr and Hf by fractional crystallization of K₂Zr(Hf)F₆. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011