Implementation and Performance of DFT-D with Respect to Basis Set and Functional for Study of Dispersion Interactions in Nanoscale Aromatic Hydrocarbons

Adsorption of molecular hydrogen on Be3Al2(SiO3)6-beryl: theoretical insights for catalysis, hydrogen storage, gas separation, sensing, and environmental applications

Employing a combination of Density Functional Theory (DFT) calculations and Molecular Dynamics (MD) simulations, the adsorption of molecular hydrogen (H2) on Be3Al2(SiO3)6-beryl, a prominent silicate mineral, has been studied. The crystal structure of beryl, which consists of interconnected tetrahedral and octahedral sites, provides a fascinating framework for comprehending H2 adsorption behavior. Initial investigation of the interaction between H2 molecules and the beryl surface employed DFT calculations. We identified favorable adsorption sites and gained insight into the binding mechanism through extensive structural optimizations and energy calculations. H2 molecules preferentially adsorb on the exposed oxygen atoms surrounding the octahedral sites, producing weak van der Waals interactions with the beryl surface, according to our findings. To further investigate the dynamic aspects of H2 adsorption, MD simulations employing a suitable force field were conducted. To precisely represent interatomic interactions within the Be3Al2(SiO3)6-beryl-H2 system, the force field parameters were meticulously parameterized. By subjecting the system to a variety of temperatures, we were able to obtain valuable information about the stability, diffusion, and desorption kinetics of H2 molecules within the beryl structure. The comprehensive understanding of the H2 adsorption phenomenon on Be3Al2(SiO3)6-beryl is provided by the combined DFT and MD investigations. The results elucidate the mechanisms underlying H2 binding, highlighting the role of surface oxygen atoms and the effect of temperature on H2 dynamics. This research contributes to a fundamental understanding of hydrogen storage and release in beryllium-based silicates and provides valuable guidance for the design and optimization of materials for hydrogen storage, catalysis, gas separation, sensing and environmental applications.

Relayed Heteroatom Group Transfer: A Structural Reorganization between Bisthioester and Triaminophosphine to α,α-Disulfenylamide

Simultaneous multiple displacements of organic molecules can lead to a large structural reconstruction with increased complexity that would be difficult to access otherwise. Whereas double displacement such as olefin metathesis is well-established, higher-order versions remain much more challenging, because of their intrinsic thermodynamic disadvantages. Here, we describe a newly discovered relayed heteroatom group transfer process between bisthioesters and triaminophosphines as an unusual example of a formal triple displacement. Through the oxygen/nitrogen exchange between the two simple starting materials, in addition to the 1,2-sulfur migration of a putative carbene intermediate, an organized relocation of the O/S/N groups proceeded to give a variety of α,α-disulfenylamides with excellent efficiency under ambient conditions. The experimental and computational mechanistic studies revealed the sequence of the relayed group shifts via an α,α-disulfenyl phosphonium enolate intermediate as well as the dual role of triaminophosphine as both an oxygen acceptor and a nitrogen donor.

Fluorine-Assisted Rearrangement of Geminal Azidofluorides to Imidoyl Fluorides

Organoazide rearrangement constitutes versatile synthetic strategies but typically requires an extremely strong acid and/or a high reaction temperature. Our group recently discovered the remarkable accelerating effect of the geminal fluorine substituent that enables the facile rearrangement of azides into imidoyl fluorides without the aid of acid under much milder reaction conditions. The role of geminal fluorine was elucidated by both experimental and computational investigations. This new reactivity led to the development of a practical one-step tandem preparative method for potentially useful and bench-stable imidoyl fluorides from a wide range of structurally diverse geminal chlorofluorides. Our additional efforts to expand the reaction scope regarding the migrating group, halogen, and carbonyl function are described, and the synthetic utility of the imidoyl fluoride products was demonstrated in hopes of promoting the use of this under-appreciated functional group in the synthetic organic community.

A Buckycatcher in Solution-A Computational Perspective

In this work, we study the buckycatcher (C₆₀H₂₈) in solution using quantum chemical models. We investigate the conformational equilibria in several media and the effects that molecules of solvent might have in interconversion barriers between the different conformers. These are studied in a hypothetical gas phase, in the dielectric of a solvent, as well as with hybrid solvation. In the latter case, due to a disruption of π-stacking interactions, the transition states are destabilized. We also evaluate the complexation of the buckycatcher with solvent-like molecules. In most cases studied, there should be no adducts formed because the enthalpy driving force cannot overcome entropic penalties.

α-Fluoroamine synthesis via P(III)-mediated deoxygenative geminal fluorosulfonimidation of 1,2-diketones

A deoxygenative geminal fluorosulfonimidation of 1,2-diketones was achieved for the synthesis of tetrasubstituted α-fluoroamines under mild conditions. In this study, a transition metal-free formal N-F insertion of N-fluorobenzenesulfonimide was enabled via the Kukhtin-Ramirez reaction employing a dealkylation-resistant P(III) reagent developed in our laboratory. Computational analysis was also performed to obtain a general mechanistic picture, which explained the reactivity and selectivity for this type of reaction.

Synthesis of α-Ketoimidoyl Fluorides via Geminal Fluorine-Promoted Azide Rearrangement

Despite the promising synthetic potential, the utilization of imidoyl fluorides has been hampered by the lack of broadly applicable preparative methods. Herein, bench-stable α-ketoimidoyl fluorides were synthesized from geminal chlorofluorides through tandem azidation/rearrangement under mild conditions. The efficiency was consistently high, regardless of the steric and electronic environments. The synthetic utility of the α-ketoimidoyl fluoride was also demonstrated. Furthermore, the remarkable accelerating effect of the geminal fluorine substituent was identified and rationalized by density functional theory calculation.

Boron nitride nanotube precursor formation during high-temperature synthesis: kinetic and thermodynamic modelling

We performed integrated modelling of the chemical pathways of formation for boron nitride nanotube (BNNT) precursors during high-temperature synthesis in a B/N₂mixture. Integrated modelling includes quantum chemistry, Quantum-classical molecular dynamics, thermodynamic modelling, and kinetic approaches. We demonstrate that BN compounds are formed via the interaction of molecular nitrogen with small boron clusters, rather than through interactions with less reactive liquid boron. (This process can also be described as N₂molecule fixation.) Liquid boron evaporates to produce these boron clusters (B_mwithm≤ 5), which are subsequently converted into B_mN_nchains. The production of such chains is crucial to the growth of BNNTs because these chains form the building blocks of bigger and longer BN chains and rings, which are in turn the building blocks of fullborenes and BNNTs. Additionally, kinetic modelling revealed that B₄N₄and B₅N₄species in particular play a major role in the N₂molecule fixation process. The formation of these species via reactions with B₄and B₅clusters is not adequately described under the assumption of thermodynamic equilibrium, as is demonstrated in our kinetic modelling. Thus, the accumulation of both B₄N₄and B₅N₄depends on the background gas pressure and the gas cooling rate. Long BN chains and rings, which are precursors of the fullborene and BNNT growth, form via self-assembly of components B₄N₄and B₅N₄. Our modelling results-particularly the increased densities of B₄N₄and B₅N₄species at higher gas pressures-explain the experimentally observed effect of gas pressure on the yield of high-quality BNNTs. The catalytic role of hydrogen was also studied; it is shown that HBNH molecules can be the main precursor of BNNT synthesis in the presence of hydrogen.

Computational modelling of Pd-catalysed alkoxycarbonylation of alkenes and alkynes

This perspective highlights the computational modelling of alkene and alkyne alkoxycarbonylation at palladium catalysts. We cover studies on Pd-catalysed alkoxycarbonylation of alkenes with bidentate diphosphine ligands, which reveal a hydride pathway is operating with an intermolecular alcoholysis step, where explicit solvation is mandatory to estimate the overall barriers correctly and model alcoholysis/copolymerisation selectivities. Subsequently, we discuss Pd-catalysed alkyne alkoxycarbonylation with P,N-chelating ligands, where an in situ base mechanism is operating involving ketene-type intermediates. We also discuss catalyst poisoning due to allene and designing a potential new catalyst tolerant towards allene poisoning.

Contributions of IQA electron correlation in understanding the chemical bond and non-covalent interactions

The quantum topological energy partitioning method Interacting Quantum Atoms (IQA) has been applied for over a decade resulting in an enlightening analysis of a variety of systems. In the last three years we have enriched this analysis by incorporating into IQA the two-particle density matrix obtained from Møller–Plesset (MP) perturbation theory. This work led to a new computational and interpretational tool to generate atomistic electron correlation and thus topologically based dispersion energies. Such an analysis determines the effects of electron correlation within atoms and between atoms, which covers both bonded and non-bonded “through -space” atom–atom interactions within a molecule or molecular complex. A series of papers published by us and other groups shows that the behavior of electron correlation is deeply ingrained in structural chemistry. Some concepts that were shown to be connected to bond correlation are bond order, multiplicity, aromaticity, and hydrogen bonding. Moreover, the concepts of covalency and ionicity were shown not to be mutually excluding but to both contribute to the stability of polar bonds. The correlation energy is considerably easier to predict by machine learning (kriging) than other IQA terms. Regarding the nature of the hydrogen bond, correlation energy presents itself in an almost contradicting way: there is much localized correlation energy in a hydrogen bond system, but its overall effect is null due to internal cancelation. Furthermore, the QTAIM delocalization index has a connection with correlation energy. We also explore the role of electron correlation in protobranching, which provides an explanation for the extra stabilization present in branched alkanes compared to their linear counterparts. We hope to show the importance of understanding the true nature of the correlation energy as the foundation of a modern representation of dispersion forces for ab initio, DFT, and force field calculations.

Accuracy of intermolecular interaction energies, particularly those of hetero-atom containing molecules obtained by DFT calculations with Grimme's D2, D3 and D3BJ dispersion corrections

Intermolecular interaction potentials for benzene, propane, perfluoromethane, furan, thiophene, selenophene, pyridine, phosphorine dimers and benzene-methane, benzene-chlorobenzene, benzene-bromobenzene complexes were calculated using the BLYP, B97 (B98), BP86, BPBE, PBE, PW91, B3LYP, B3PW91, BMK, PBE1PBE, APF, ωB97 (ωB97X), CAM-B3LYP, LC-ωPBE, B2PLYP, mPW2PLYP, TPSS, M06L, M05, M052X, M06, M062X and M06HF functionals with Grimme's dispersion correction methods of D2, D3 and D3BJ versions. The calculated potentials were compared with the CCSD(T) level potentials to evaluate the accuracy of the dispersion corrected DFT methods for calculating the intermolecular interaction energies of hydrocarbon molecules and molecules including heteroatoms (N, P, O, S, Se, F, Cl and Br). The performance of the calculations depends strongly on the choice of the functional and the dispersion correction method. None of the combinations of the functionals and the dispersion correction methods can reproduce well the CCSD(T) level interaction potentials of all the complexes. The improvement of the functionals from GGA to hybrid GGA, meta GGA or meta hybrid GGA is not essential for improving the performance. The significant functional dependence suggests that the scaling factors, which were determined for each functional by fitting, are the cause of the dependence. The performance of the calculations of hydrocarbon molecules is much better than that of the molecules including heteroatoms. A smaller number of molecules including heteroatoms were used for the reference data of the fitting compared with hydrocarbon molecules, which might be one of the causes of the worse performance of the calculations of molecules including heteroatoms.

Deciphering the Origin of Enantioselectivity on the Cis-Cyclopropanation of Styrene with Enantiopure Di-chloro,Di-gold(I)-SEGPHOS Carbenoids Generated from Propargylic Esters

The stereoselective synthesis of cis-disubstituted cyclopropanes by the Au(I)/PPh₃-catalyzed cycloaddition of propargylic esters and styrene has been studied using density functional theory calculations. The computed mechanistic scheme involves the rate-limiting 1,2-rearrangement of the propargylic ester with the π-coordinated gold complex, followed by the (2 + 1)-cheletropic reaction of styrene with the alkenyl-Au(I) carbene intermediate to afford the cis-disubstituted cyclopropane derivative in a high cis/trans diastereomeric ratio. With a ( R)-di-chloro,di-gold-DTBM-SEGPHOS complex as the catalyst, computations are consistent with a rate-determining (2 + 1)-cheletropic reaction, in which facial discrimination is proposed to result from a combination of subtle steric and electronic effects in the SiRe facial approach transition structure, which favor the formation of the cis-cyclopropane diastereomer of 1 R,2 S absolute configuration, as experimentally observed.

DFT Computed Dielectric Response and THz Spectra of Organic Co-Crystals and Their Constituent Components

Terahertz (THz) spectroscopy has been put forth as a non-contact, analytical probe to characterize the intermolecular interactions of biologically active molecules, specifically as a way to understand, better develop, and use active pharmaceutical ingredients. An obstacle towards fully utilizing this technique as a probe is the need to couple features in the THz regions to specific vibrational modes and interactions. One solution is to use density functional theory (DFT) methods to assign specific vibrational modes to signals in the THz region, coupling atomistic insights to spectral features. Here, we use open source planewave DFT packages that employ ultrasoft pseudopotentials to assess the infrared (IR) response of organic compounds and complex co-crystal formulations in the solid state, with and without dispersion corrections. We compare our DFT computed lattice parameters and vibrational modes to experiment and comment on how to improve the agreement between theory and modeling to allow for THz spectroscopy to be used as an analytical probe in complex biologically relevant systems.

Conjugated microporous polymer nanosheets and nanotubes as novel absorbents for microcystin-LR: insights from theoretical investigations

Our calculations demonstrated that CMP nanosheet and nanotube materials can be developed as novel adsorbents for harmful microcystin-LR adsorption/removal.

Potential models for the simulation of methane adsorption on graphene: development and CCSD(T) benchmarks

Different force fields for the graphene-CH4 system are proposed including pseudo-atom and full atomistic models. Furthermore, different charge schemes are tested to evaluate the electrostatic interaction for the CH4 dimer. The interaction parameters are optimized by fitting to interaction energies at the DFT level, which were themselves benchmarked against CCSD(T) calculations. The potentials obtained with both the pseudo-atom and full atomistic approaches describe accurately enough the average interaction in the methane dimer as well as in the graphene-methane system. Moreover, the atom-atom potentials also correctly provide the energies associated with different orientations of the molecules. In the atomistic models, charge schemes including small charges allow for the adequate representation of the stability sequence of significant conformations of the methane dimer. Additionally, an intermediate charge of -0.63e on the carbon atom in methane leads to bond energies with errors of ca. 0.07 kcal mol-1 with respect to the CCSD(T) values for the methane dimer. For the graphene-methane interaction, the atom-atom potential model predicts an average interaction energy of 2.89 kcal mol-1, comparable to the experimental interaction energy of 3.00 kcal mol-1. Finally, the presented force fields were used to obtain self-diffusion coefficients that were checked against the experimental value found in the literature. The no-charge and Hirshfeld charge atom-atom models perform extremely well in this respect, while the cheapest potential considered, a pseudo-atom model without charges, still performs reasonably well.

Heterometallic Palladium(II)-Indium(III) and -Gallium(III) Acetate-Bridged Complexes: Synthesis, Structure, and Catalytic Performance in Homogeneous Alkyne and Alkene Hydrogenation

The reaction of Pd₃(OOCMe)₆ with indium(III) and gallium(III) acetates was studied to prepare new Pd^II-based heterometallic carboxylate complexes with group 13 metals. The heterometallic palladium(II)-indium(III) acetate-bridged complexes Pd(OOCMe)₄In(OOCMe) (1) and Pd(OOCMe)₄In(OOCMe)·MeCOOH (1a) were synthesized and structurally characterized with X-ray crystallography and extended X-ray absorption fine structure in the solid state and solution. A similar Pd-Ga heterometallic complex formed by the reaction of Pd₃(OOCMe)₆ with gallium(III) acetate in a dilute acetic acid solution, as evidenced by atmospheric pressure chemical ionization mass and UV-vis spectrometry, was unstable at higher concentrations and in the solid state. Complex 1 catalyzes the liquid-phase-selective phenylacetylene and styrene hydrogenation (1 atm of H₂ at 20 °C) in acetic acid, ethyl acetate, and N, N-dimethylformamide solutions, while no Pd metal was formed until alkyne and alkene hydrogenation ceased.

Composite and Low-Cost Approaches for Molecular Crystal Structure Prediction

Molecular crystal structure prediction (CSP) requires evaluating differences in lattice energy between candidate crystal structures accurately and efficiently. In this work, we explore and compare several low-cost alternatives to dispersion-corrected density-functional theory (DFT) in the plane-waves/pseudopotential approximation, the most accurate and general approach used for CSP at present. Three types of low-cost methods are considered: DFT with a small basis set of finite-support numerical orbitals (the SIESTA method), dispersion-corrected Gaussian small or minimal-basis-set Hartree-Fock and DFT with additional empirical corrections (HF-3c and PBEh-3c), and self-consistent-charge dispersion-corrected density-functional tight binding (SCC-DFTB3-D3). In addition, we study the performance of composite methods that comprise a geometry optimization using a low-cost approach followed by a single-point calculation using the accurate but comparatively expensive B86bPBE-XDM functional. All methods were tested for their abilities to produce absolute lattice energies, relative lattice energies, and crystal geometries. We show that assessing various methods by their ability to produce absolute lattice energies can be misleading and that relative lattice energies are a much better indicator of performance in CSP. The EE14 set of relative solubilities of homochiral and heterochiral chiral crystals is proposed for relative lattice-energy benchmarking. Our results show that PBE-D2 plus a DZP basis set of numerical orbitals coupled with a final B86bPBE-XDM single-point calculation gives excellent performance at a fraction of the cost of a full B86bPBE-XDM calculation, although the results are sensitive to the particular details of the computational protocol. The B86bPBE-XDM//PBE-D2/DZP method was subsequently tested in a practical CSP application from our recent work on the crystal structure of the enantiopure and racemate forms of 1-aza[6]helicene, a chiral organic semiconductor. Our results show that this multilevel method is able to correctly reproduce the energy ranking of both crystal forms.

Collision-induced activation: Towards industrially scalable approach to graphite nanoplatelets functionalization for superior polymer nanocomposites

Scale-up manufacturing of engineered graphene-like nanomaterials to deliver the industry needs for development of high-performance polymer nanocomposites still remains a challenge. Herein, we introduce a quick and cost-effective approach to scalable production of functionalized graphite nanoplatelets using "kitchen blender" approach and Diels-Alder chemistry. We have shown that, in a solvent-free process and through a cycloaddition mechanism, maleic anhydride can be grafted onto the edge-localized electron rich active sites of graphite nanoplatelets (GNP) resulting from high collision force, called "graphite collision-induced activation". The mechanical impact was modelled by applying the point charge method using density functional theory (DFT). The functionalization of GNP with maleic anhydride (m-GNP) was characterized using various spectroscopy techniques. In the next step, we used a recyclable process to convert m-GNP to the highly-reactive GNP (f-GNP) which exhibits a strong affinity towards the epoxy polymer matrix. It was found that at a low content of f-GNP e.g., 0.5 wt%, significant enhancements of ~54% and ~65% in tensile and flexural strengths of epoxy nanocomposite can be achieved, respectively. It is believed that this new protocol for functionalization of graphene nanomaterials will pave the way for relatively simple industrial scale fabrication of high performance graphene based nanocomposites.

Corannulene and its complex with water: a tiny cup of water

We report the results of a broadband rotational spectroscopic study of corannulene, C₂₀H₁₀, all of its singly substituted ¹³C isotopologues, and a complex of corannulene with one molecule of water.

Experimental and theoretical insight into the effect of fluorine substituents on the properties of azine linked covalent organic frameworks

Herein we report a combined experimental and computational study on the effect of fluorine atom incorporation on the materials properties of azine-linked COFs.

Synergy between experimental and computational studies of aromatic stacking interactions

Aromatic stacking interactions are one of the most common types of non-covalent interactions. However, their fundamental origins and the ability to accurately predict their stability trends are still an active area of research. The study of aromatic stacking interactions has been particularly challenging. The interaction involves a delicate balance of multiple forces, and the aromatic surfaces can readily adopt different interaction geometries. Thus, the collaborative efforts of theoretical and experimental researchers have been essential to understand and build more accurate predictive models of aromatic stacking interactions.

Theoretical Studies of the Stone-Wales Defect in C36 Fullerene Embedded inside Zigzag Carbon Nanotube

We apply density functional theory at PBE/6-311G(d) level as well as nonorthogonal tight-binding model to study the Stone-Wales transformation in C36 fullerene embedded inside the (14,0) zigzag carbon nanotube. We optimize geometries of two different isomers with the D2d and the D6h symmetries and the transition state dividing them. The mechanism of Stone-Wales transformation from D2d to D6h symmetry for the encapsulated C36 is calculated to be the same as for the isolated one. It is found that the outer carbon wall significantly stabilizes the D6h isomer. However, carbon nanotube reduces the activation barrier of Stone-Wales rearrangement by 0.4 eV compared with the corresponding value for the isolated C36.

Catalytic enantioselective epoxidation of nitroalkenes

Nitroepoxides are potentially exploitable as synthons with vicinal electrophilic centers.

Theoretical studies on a carbonaceous molecular bearing: association thermodynamics and dual-mode rolling dynamics

The thermodynamics and dynamics of a carbonaceous molecular bearing comprising a belt-persistent tubular molecule and a fullerene molecule have been investigated using density functional theory (DFT). Among ten representative methods, two DFT methods afforded an association energy that reasonably reproduced the experimental enthalpy of -12.5 kcal mol-1 at the unique curved π-interface. The dynamics of the molecular bearing, which was assembled solely with van der Waals interactions, exhibited small energy barriers with maximum values of 2-3 kcal mol-1 for the rolling motions. The dynamic motions responded sensitively to the steric environment and resulted in two distinct motions, precession and spin, which explained the unique NMR observations that were not clarified in previous experimental studies.

Conformational studies of poly(vinylidene fluoride), poly(trifluoroethylene) and poly(vinylidene fluoride-co-trifluoroethylene) using density functional theory

Different conformations of systems consisting of poly(vinylidene fluoride) (PVDF), poly(trifluoroethylene) (PTrFE) and poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-TrFE)) were investigated using density functional theory with dispersion correction. It was found that the trans-gauche-trans-gauche' (TGTG') conformation of a single PVDF chain is the lowest energy conformer. Crystals of PVDF were modelled using between two to five chains with up to 12 repeat units in each chain and, in agreement with experiment, structures comprised partly or completely of chains with the TGTG' conformation are more stable than structures built up from chains with all-trans (TTTT) conformation. This indicates that an all-trans segment or chain will not induce the growth of a larger crystal with the same chain conformations. In contrast, the energetically preferred structure of PTrFE chains is an all-trans (TTTT) conformation, and the results indicate that copolymerization of vinylidene fluoride with trifluoroethylene can facilitate the formation of the all-trans PVDF conformations. This is probably due to increased intramolecular repulsion between the fluorine atoms and an increased intermolecular attraction in the crystal structure.