DFT Protocols Research Articles

Knotted or unknotted? A theoretical quantum protocol for luminescence simulation of metallo-supramolecular knots

Entangled structures are topological architectures often observed not only in the macroscopic world, but also at the molecular level with many examples in biological systems (DNA, RNA). In recent decades, these fascinating entities have aroused considerable interest among chemists with the advent of metallo-supramolecular knots. Notwithstanding the burgeoning of such metal complexes in literature, their use as luminescent emitters as well as systematic studies on their luminescence properties are still extremely limited. In view of this, a theoretical DFT protocol dedicated to luminescence profile simulations of these peculiar “entwined” species is highly desirable. In this work, we propose a robust and affordable DFT computational workflow able to recreate meticulously the emission band-shape of different metallo-supramolecular knots. As a result of a preparatory DFT benchmark, we decided to use HSEH1PBE/LanL2DZ level via Born-Oppenheimer molecular dynamics to explore the change in the coordination environment around the metal centers in the excited state (S1). Thereupon, a detailed recruiting of TD-DFT functionals recommended the mPW3PBE/LanL2DZ level as the most precise and transferable method to model accurately metallo-supramolecular knots emission spectra as metal ions, internal spacers and interlocking modes vary.

Response surface and DFT protocols for improvement of the adsorption process of lignocellulosic-based biomass for the removal of basic dyes

Jatobá-do-cerrado fruit shells, archetypical of lignocellulosic-based biomass, were used as an adsorbent to remove crystal violet (CV) and methylene blue (MB) from water. The adsorbent was characterized using various techniques, and kinetic studies showed dye adsorption followed second-order kinetics. An experimental design investigated the effects of pH and temperature on removal efficiency, with a quadratic model fitting the data best. The results suggest pH influences MB's adsorption capacity more than temperature and at 25 °C and pH 8, MB had a desirability value of 0.89, with 95 % removal efficiency. For CV, temperature had a greater influence, with a desirability value of 0.874 at 25 °C and pH 10, and 95 % removal efficiency. Adsorption isotherm studies revealed maximum adsorption capacities of 123.0 mg·g−1 and 113.0 mg·g−1 for CV and MB, respectively. Experimental thermodynamic parameters indicated an endothermic and spontaneous process which it was supported by quantum chemistry calculations. The protocols developed confirmed the potential for adsorbing CV and MB dyes in water, achieving over 73.1 and 74.4 mg g−1 dyes removal.

From a humorous post to a detailed quantum-chemical study: isocyanate synthesis revisited.

Isocyanates play an essential role in modern manufacturing processes, especially in polyurethane production. There are numerous synthesis strategies for isocyanates both under industrial and laboratory conditions, which do not prevent searching for alternative highly efficient synthetic protocols. Here, we report a detailed theoretical investigation of the mechanism of sulfur dioxide-catalyzed rearrangement of phenylnitrile oxide into phenyl isocyanate, which was first reported in 1977. The DLPNO-CCSD(T) method and up-to-date DFT protocols were used to perform a highly accurate quantum-chemical study of the rearrangement mechanism. An overview of various organic and inorganic catalysts has revealed other potential catalysts, such as sulfur trioxide and selenium dioxide. Furthermore, the present study elucidated how substituents in phenylnitrile oxide influence reaction kinetics. This study was performed by a self-organized collaboration of scientists initiated by a humorous post on the VK social network.

Pushing measurements and interpretation of VCD spectra in the IR, NIR and visible ranges to the detectability and computational complexity limits

(R)-Limonene VCD and IR absorption spectra for neat liquid samples are considered from 900 to 16,000 cm−1, using mostly data by Nafie et al. up to 10,000 cm−1 and from previous investigations of the Brescia group. New VCD data are recorded in the merely overtone and combination region between 1800 and 2400 cm−1 and for the Δn= 6 overtone CH-stretching region above 15,000 cm−1. The GVPT2 anharmonic DFT calculations permit satisfactory interpretation of the fundamental + overtone/combination of deformation modes in the mid-IR up to 3500 cm−1. The GVPT2 approach is also used for the first CH-stretching overtone regions together with their combination with deformation modes up to 9000 cm−1. Then the local-mode approach developed within the DFT protocol is employed in all the CH-stretching regions (fundamental + overtones) and is found to satisfactorily account for the observed spectra, justifying the constant VCD pattern observed for all overtones. On the basis of the local-mode model the components of the bisignate VCD spectrum are attributed to the stretchings of the axial and equatorial CH bonds in α-position with respect to the ring CC double bond.

Angewandte Chemie: A Team Effort

<i>Angewandte Chemie</i>: A Team Effort

Insights into the value of statistical models, solvent, and relativistic effects for investigating Re complexes of 2-(4'-aminophenyl)benzothiazole: a potential spectroscopic probe.

Cancer affects a major part of the worldwide population, and, to minimize deaths, the diagnosis in the early stages of the disease is fundamental. Thus, to improve diagnosis and treatment new potential spectroscopic probes are crucial. Benzothiazole derivates present antitumor properties and are highly selective and interact strongly with the enzyme phosphoinositide 3-kinase (PI3K), which was associated with cell proliferation and breast cancer cells. In this paper, the rhenium shielding tensors (187Re(σ)) and hydrogen and carbon chemical shifts (1H(δ) and 13C(δ)) of the Re(CO)3(NNO) complex conjugated with 2-(4'-aminophenyl)benzothiazole (ReABT) were evaluated. A statistical HCA model was used to analyze the best DFT protocol to compute σ and δ values and to evaluate the relativistic effects, both in the basis set and Hamiltonian as well as the functionals M06L or PBE0. The best protocol was applied to obtain 187Re(σ) of the ReABT complex in different environments (gas phase, solution, and in the active site of the PI3K enzyme). The results point out that 187Re(σ) values of the ReABT complex change significantly when the complex is docked in the PI3K enzyme.

Combined DFT and MD Simulation Protocol to Characterize Self-Healing Properties in Disulfide-Containing Materials: Polyurethanes and Polymethacrylates as Case Studies

The introduction of dynamic bonds in polymeric materials facilitates the emergence of new functionalities, such as self-healing capacity. Understanding the role of the molecular structure in the efficiency of the self-healing process is fundamental to design new materials with improved features. Computational chemistry has emerged as a valuable tool for the characterization of polymeric materials. In this work, computational chemistry is used to analyze the observed self-healing capacity of a set of disulfide-containing polyurethanes and polymethacrylates, including different hard segments and dynamic bonds. For this purpose, a recently developed theoretical protocol has been used. This protocol is based on three parameters: the probability of generating radicals by cleavage of the disulfide bond, the energetic barrier of the exchange reaction among disulfides and the dynamics of the polymeric chains. This protocol is able to qualitatively explain the experimental self-healing properties of these materials. In particular, it explains both the great performance of two materials and the lack of self-healing capacity of another two. Besides, it can also describe the improvement of the self-healing capacity with increasing temperature. These results demonstrate the robustness and usefulness of this approach for the analysis and prediction of self-healing properties in polymeric materials. Therefore, this protocol allows to predict new materials with improved properties and will help the experimental community in the development of these improved materials.

OH-Initiated Reactions of p-Coumaryl Alcohol Relevant to the Lignin Pyrolysis. Part I. Potential Energy Surface Analysis ⊥.

Cinnamyl alcohols such as p-coumaryl alcohol ( p-CMA) are lignin models and precursors (monolignols) and the most important primary products of lignin pyrolysis. However, the detection of monomers is not straightforward since they either undergo secondary transformations or repolymerize to contribute to the char formation. Both concerted-molecular and free-radical pathways are involved in these processes. Our recent fundamentally based theoretical and low-temperature matrix-isolation-EPR studies of cinnamyl alcohols highlighted the role of side-chain reactivity in diversity of pyrolysis products and provided a network of the chemically activated H + p-CMA reactions ( Asatryan J. Phys. Chem. A, 2017 , 121 , 3352 - 3371 ). The readily available hydroxyl radicals also can trigger a cascade of free-radical processes. Here, we present a comprehensive potential energy surface (PES) analysis of the OH + p-CMA reaction using various DFT and ab initio protocols. Since the p-CMA involves both an alkyl OH-group and a side-chain double bond, the title reaction can also serve as a relevant model for reactions of unsaturated alcohols with hydroxyl radicals to form various oxygenates including polyhydric alcohols which are abundant in nature. The newly identified pathways suggest certain alternatives to the known radical reactions. Of particular interest are the roaming-like low-energy dehydration reactions to generate a variety of O- and C-centered intermediate radicals, which are primarily transformed into the phenolic compounds observed in pyrolysis experiments. Several concerted unimolecular decomposition pathways for p-CMA are also revealed, not considered previously, such as the migration of terminal OH-group, and/or its splitting over the ipso-C and ortho-C atoms of the benzene ring to form bicyclic oxispiro- and chromene compounds represented in natural lignin.

Molecular Products and Fundamentally Based Reaction Pathways in the Gas-Phase Pyrolysis of the Lignin Model Compound p-Coumaryl Alcohol.

The fractional pyrolysis of lignin model compound para-coumaryl alcohol (p-CMA) containing a propanoid side chain and a phenolic OH group was studied using the System for Thermal Diagnostic Studies at temperatures from 200 to 900 °C, in order to gain mechanistic insight into the role of large substituents in high-lignin feedstocks pyrolysis. Phenol and its simple derivatives p-cresol, ethyl-, propenyl-, and propyl-phenols were found to be the major products predominantly formed at low pyrolysis temperatures (<500 °C). A cryogenic trapping technique was employed combined with EPR spectroscopy to identify the open-shell intermediates registered at pyrolysis temperatures above 500 °C. These were characterized as radical mixtures primarily consisting of oxygen-linked conjugated radicals. A comprehensive potential energy surface analysis of p-CMA and p-CMA + H atom systems was performed using various DFT protocols to examine the possible role of concerted molecular eliminations and free-radical mechanisms in the formation of major products. Other significant unimolecular concerted reactions along with formation and decomposition of primary radicals are also described and evaluated. The calculations suggest that a set of the chemically activated secondary radical channels is relevant to the low temperature product formation under fractional pyrolysis conditions.

DFT Analysis of Spin Crossover in Mn(III) Complexes: Is a Two-Electron S = 2 to S = 0 Spin Transition Feasible?

Six-coordinate, rigorously octahedral d4 Mn(III) spin crossover (SCO) complexes are limited by symmetry to an S = 1 (intermediate spin, IS) to S = 2 (high spin, HS) transition. In order to realize the potential S = 0 to S = 2 transition, a lower symmetry and/or change in coordination number is needed, which we explore here computationally. First, a number of complexes are analyzed to develop a reliable and relatively fast DFT protocol for reproducing known Mn(III) spin state energetics. The hybrid meta-GGA functional TPSSh with a modest split valence plus polarization basis set and an empirical dispersion correction is found to predict correctly the ground spin state of Mn(III) complexes, including true low-spin (LS) S = 0 systems, with a range of donor sets including the hexadentate [N4O2] Schiff base ligands. The electronic structure design criteria necessary for realizing a ΔS = 2 SCO transition are described, and a number of model complexes are screened for potential SCO behavior. Five-coordinate trigonal-bipyramidal symmetry fails to yield any suitable systems. Seven-coordinate, approximately pentagonal bipyramidal symmetry is more favorable, and when a known pentadentate macrocyclic donor is combined with π-acceptor axial ligands, a novel Mn(III) complex, [Mn(PABODP)(PF3)2]3+ (PABODP = 2,13-dimethyl-3,6,9,12,18-pentaazabicyclo[12.3.1]octadeca-1(18),2,12,14,16-pentaene), is predicted to have the right spin state energetics for an S = 0 to S = 2 transition. Successful synthesis of such a complex could provide the first example of a ΔS = 2 SCO transition for d4 Mn(III). However, the combination of a rigid macrocycle and a high coordination number dilutes the stereochemical activity of the d electrons, leading to relatively small structural changes between HS and LS systems. It may therefore remain a challenge to realize strong cooperative effects in Mn(III) systems.

Synthesis of a new heterocyclic Schiff base ligand “(E)-5-benzoyl-4-phenyl-1-((pyridin-2-ylmethylene) amino) pyrimidin-2(1H)-one”: An experimental and computational modeling study

In this study, a new heterocyclic Schiff base has been synthesized and characterized using FT-IR, NMR (1H NMR, 13C NMR), UV–Vis, Mass spectroscopies and single-crystal X-ray diffraction method. The molecular geometry obtained from the X-ray structure determination was optimized using Density Functional Theory (DFT/B3LYP) method with the 6-31G+(d, p) basis set in ground state. From the optimized geometry of the title molecule, the geometric parameters (bond lengths, bond angles and torsion angles), vibrational wavenumbers and chemical shifts were computed. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMOs) and nonlinear optical (NLO) property of this molecule were determined using a DFT protocol at the B3LYP/6-31+G (d, p) level. For the purpose of the structural conformity of the title molecule, the theoretical results were compared with the experimental values. This comparison indicated that the theoretically calculated results are in agreement with the experimental data on the whole.

DFT calculation of NMR δ(113Cd) in cadmium complexes

We have tested several DFT protocols, at the non-relativistic and relativistic ZORA (scalar and spin–orbit) levels, for the calculation of the 113Cd chemical shifts, δ(113Cd), for a number of cadmium complexes accounting for both different local coordination environments on the metal center, involving N, O and S ligands, and different geometrical arrangements. Moreover, suitable models as reference compounds for δ(113Cd) evaluation have been set up in order to propose a complete computational approach to calculate δ(113Cd) for cadmium complexes. Inclusion of relativistic corrections did not lead to any sensible improvement in the quality of results and, in this context, non-relativistic method, namely: B3LYP/Sadlej(Cd); 6-31g(d,p) (light atoms), showed to be the best approach to calculate δ(113Cd) for the classes of compounds investigated.

A DFT study of the vicinal 3J(119Sn,13C) and 3J(119Sn,1H) coupling constants in trimethyl- and chlorodimethylstannyl propanoates

We have tested the performance of DFT protocols, both at the Scalar relativistic ZORA and non-relativistic level of theory, for the calculation of the 3J(119Sn,13C) and 3J(119Sn,1H) vicinal couplings for a series of flexible organotin(IV) derivatives with formula XMe2SnCHRCHR′COOMe (X=Me, Cl; R, R′=Me, Ph). A satisfactory agreement between experimental and calculated vicinal couplings has been obtained by taking into account the conformational behaviour of the compounds investigated. The protocols used, mainly the relativistic one, were found to give a correct picture of the populations and a sufficiently high overall performance in calculating the vicinal couplings, thereby overcoming the use of empirical Karplus-type relationships to infer geometrical parameters from 3J(119Sn,13C) and 3J(119Sn,1H).

Theoretical study of the anthropogenic greenhouse gas (SF5CF3) and analysis of the reaction of SF6 with CF

AbstractSF5CF3 was recently detected in the earth's atmosphere. This has lead to various experimental and theoretical studies aimed at establishing the properties of this molecule, from which to understand how it is formed, how it may impact on the atmosphere (it is a powerful greenhouse gas), and how it may be destroyed in the atmosphere. SF5CF3 is chemically very inert, and is not destroyed in the troposhere. Theoretical calculations using effective core potential (ECP) based on high‐level methods — QCISD(T), were performed for molecular systems related to SF5CF3. Existing values for the S–C bond dissociation energy in SF5CF3 span a wide range, from estimates of about 200 to 300 kJ mol−1, obtained from theoretical calculations on SF5CF3 using the DFT, G2, and G3 protocols, to 390 ± 45 kJ mol−1 derived from experimental studies of the photoionisation of SF5CF3. At the QCISD(T)/ECP + GCM (generator coordinate method) level, the dissociation energy ‐ Do (SF5 ‐CF3, 0 K), is 274.7 kJ mol−1. In addition to calculations on individual molecules, the reactions of SF6 with CF were studied. The first objective was to locate the reactant ion‐molecule complex, the transition state, and the product ion‐molecule complex for each of these systems. On the basis of literature thermochemistry, the reaction of SF6 with CF, in which the CF reactant anion abstracts F+ from SF6 to leave SF, is highly exothermic (−343 kJ mol−1). At the QCISD(T)/ECP + GCM level gives a value of −377.6 kJ mol−1. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

DFT study of the interaction free energy of π–π complexes of fullerenes with buckybowls and viologen dimers

We present a theoretical investigation, by means of DFT protocols, of the complexation thermodynamics of (i) complexes of C70 and C60 fullerenes with bowl-shaped hexabenzocoronene derivatives and (ii) complexes of C60 with viologen dimers. The recent functionals of the M06 family, accounting for π–π interactions to a good level of approximation, have been used to calculate the interaction free energies. For the former complexes, the good agreement between the calculated results and the experimental data confirms the reliability of the protocol used. On these grounds, we then checked the stability of a series of complexes of C60 with some viologen dimers, 1BPnBP1 (n = 6–9), where two N-methylated bipyridinium units are linked by an alkyl chain of variable length, acting as molecular tweezers. Both forms of the viologen cores, that is the cation (each core doubly charged) and the reduced neutral form, were considered. For a suitable chain length a free energy gain upon complexation is predicted for the neutral form while the complexation of C60 by the cationic form is disfavoured mainly for entropic reasons.

A DFT study of the Karplus-type dependence of vicinal 3J(Sn–C-X-C), X=N,O,S, in organotin(iv) compounds: application to conformationally flexible systems

ZORA relativistic and non-relativistic DFT protocols have been used to investigate vicinal coupling constants, (3)J(Sn-C-X-C), in several organotin(iv) compounds, with particular emphasis on cyclic alpha-aminoorganostannanes. The dependence of the coupling constant on the heteroatom X (X = N,O,S) in the coupling path, and, for X = N, its substituents, has been studied in detail. The electron-withdrawing strength of the N-substituents has been found to strongly affect the magnitude and shape of the Karplus-type curve. The results obtained for the simple model systems, having no or little conformational flexibility, have helped in rationalizing the data concerning real flexible cyclic systems recently investigated in the literature. For these intricate cases a population analysis of various conformers has allowed to obtain a very good agreement between calculated and experimental data. It is therefore established that NMR J couplings, together with DFT calculations, are a very useful tool to investigate conformational issues in solution by comparison of experimental and weighted average calculated values.

Characterization and Electronic Structures of Five Members of the Electron Transfer Series [Re(benzene-1,2-dithiolato)3]z (z = 1+, 0, 1−, 2−, 3−): A Spectroscopic and Density Functional Theoretical Study

The reaction of ReCl(5) with 3 equiv of a benzene-1,2-dithiolate derivative in CH(3)CN produced, after the addition of [C(8)H(16)N]Br ([C(8)H(16)N](+) is 5-azonia-spiro[4,4]nonane), brownish-green crystals of [C(8)H(16)N][Re(tms)(3)] (1c) and [C(8)H(16)N][Re(Cl(2)-bdt)(3)] (2c), where (tms)(2-) represents 3,6-bis(trimethylsilyl)benzene-1,2-dithiolate and (Cl(2)-bdt)(2-) is 3,6-dichlorobenzene-1,2-dithiolate. Chemical reduction of [Re(bdt)(3)] (3b) with n-butyllithium in the presence of PPh(4)Br yielded [PPh(4)][Re(bdt)(3)] (3c), where (bdt)(2-) is benzene-1,2-dithiolate. The three monoanionic complexes possess a diamagnetic ground state (Re(V), d(2), S = 0). The crystal structures of 1c x 2 CH(3)CN and 2c x C(3)H(6)O have been determined by X-ray crystallography. The electrochemistry establishes that the complexes are members of electron transfer series involving a monocation [Re(V)(L(*))(2)(L)](+) (S = 0(?)), a neutral [Re(V)(L(*))(L)(2)](0) (S = 1/2), a monoanion [Re(V)(L)(3)](1-) (S = 0), a dianion [Re(IV)(L)(3)](2-) (S = 1/2), and a trianion [Re(III)(L)(3)](3-) (S = 1(?)). The unique X-band EPR spectrum of the neutral species clearly describes a diamagnetic Re(V) d(2) central ion with the unpaired electron located in a purely ligand-centered molecular orbital, whereas it is metal-centered in the dianionic form: a Re(IV) d(3) ion with three dithiolate(2-) ligands. S K-edge and Re L-edge X-ray absorption spectroscopy confirms these assignments and furthermore shows that the monoanion has a Re(V) central ion with three dianionic ligands. The geometrical and electronic structures of all members of the electron transfer series have been calculated by density functional theoretical methods, and the S K-pre-edge spectra have been simulated and assigned using a time-dependent DFT protocol.

Use of Effective Core Potential Calculations for the Conformational and Vibrational Study of Platinum(II) Anticancer Drugs. cis-Diamminedichloroplatinum(II) as a Case Study

In the light of the recognized anticancer properties of cisplatin-type inorganic systems, the exact knowledge of their conformational preferences is of the utmost importance for understanding their biological activity. The present study reports the use of theoretical (quantum mechanical) calculations for achieving this goal. An alternative calculation method to the use of the AE basis sets, both accurate and computationally feasible, was presently tested for the conformational and vibrational study of cis-diamminedichloroplatinum(II). Effective core potentials (ECPs) were used, within the HF methodology and, within the B3LYP and mPW1PW DFT protocols. The DFT methods (particularly mPW1PW) were found to be the best choice for describing cDDP (as compared to the HF methodology).

Evaluation of various DFT protocols for computing 1H and 13C chemical shifts to distinguish stereoisomers: diastereomeric 2‐, 3‐, and 4‐methylcyclohexanols as a test set

Abstract1H and 13C NMR chemical shifts were measured for a set of six isomers—the cis and trans 2‐, 3‐, and 4‐methylcyclohexanols. 1H and 13C NMR chemical shifts were computed at the B3LYP, WP04, WC04, and PBE1 density functional levels for the same compounds, taking into account the Boltzmann distribution among conformational isomers (chair–chair forms and hydroxyl rotamers). The experimental versus computed chemical shift values for proton and carbon were compared and evaluated (using linear correlation (r2), total absolute error (|Δδ|T), and mean unsigned error (MUE) criteria) with respect to the relative ability of each method to distinguish between cis and trans stereoisomers for each of the three constitutional isomers. For 13C shift data, results from the B3LYP and PBE1 density functionals were not sufficiently accurate to distinguish all three pairs of stereoisomers, while results using the WC04 functional did do so. For 1H shift data, each of the WP04, B3LYP, and PBE1 methods was sufficiently accurate to make the proper stereochemical distinction for each of the three pairs. Applying a linear correction to the computed data improved both the absolute accuracy and the degree of discrimination for most of the methods. The nature of the cavity definition used for continuum solvation had little effect. Overall, use of proton chemical shift data was more discriminating than use of carbon data. Copyright © 2007 John Wiley &amp; Sons, Ltd.

Normative Data and Interrater Reliability of the Design Fluency Test

This study generated normative data for the free and fixed conditions of the Design Fluency Test (DFT; Jones-Gotman & Milner, 1977) and investigated its interrater reliability. Three raters independently scored DFT protocols from 66 normal adults according to criteria that have only recently been published (Jones-Gotman, 1990; see Spreen & Strauss, 1998 for summary). Interrater reliability was good to excellent for novel output scores and perseverative errors, but nameable errors and designs with the incorrect number of lines yielded lower reliability coefficients. Overall, interrater reliability of the DFT appears to be relatively good, especially for the free condition and, therefore, clinical use with adequate normative data may be justified.