Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems

Vacancy impacts on electronic and mechanical properties of MX2 (M = Mo, W and X = S, Se) monolayers

Monolayers of transition metal dichalcogenides (TMD) exhibit excellent mechanical and electrical characteristics. Previous studies have shown that vacancies are frequently created during the synthesis, which can alter the physicochemical characteristics of TMDs. Even though the properties of pristine TMD structures are well studied, the effects of vacancies on the electrical and mechanical properties have received far less attention. In this paper, we applied first-principles density functional theory (DFT) to comparatively investigate the properties of defective TMD monolayers including molybdenum disulfide (MoS₂), molybdenum diselenide (MoSe₂), tungsten disulfide (WS₂), and tungsten diselenide (WSe₂). The impacts of six types of anion or metal complex vacancies were studied. According to our findings, the electronic and mechanical properties are slightly impacted by anion vacancy defects. In contrast, vacancies in metal complexes considerably affect their electronic and mechanical properties. Additionally, the mechanical properties of TMDs are significantly influenced by both their structural phases and anions. Specifically, defective diselenides become more mechanically unstable due to the comparatively poor bonding strength between Se and metal based on the analysis of the crystal orbital Hamilton population (COHP). The outcomes of this study may provide the theoretical knowledge base to boost more applications of the TMD systems through defect engineering.

Theoretical understanding of electronic and mechanical properties of 1T' transition metal dichalcogenide crystals

Transition metal dichalcogenides (TMDs) with a 1T' layer structure have recently received intense interest due to their outstanding physical and chemical properties. While the physicochemical behaviors of 1T' TMD monolayers have been widely investigated, the corresponding properties of layered 1T' TMD crystals have rarely been studied. As TMD monolayers do not have interlayer interactions, their physicochemical properties will differ from those of layered TMD materials. In this study, the electronic and mechanical characteristics of a range of 1T' TMDs are systematically examined by means of density functional theory (DFT) calculations. Our results reveal that the properties of 1T' TMDs are mainly affected by their anions. The disulfides are stiffer and more rigid, diselenides are more brittle. In addition, the 1T' polytype is softer than 2H TMDs. Comparison with the properties of the monolayers shows that the interlayer van der Waals forces can slightly weaken the TM-X covalent bonding strength, which can further influence the mechanical properties. These insights revealed by our theoretical studies may boost more applications of 1T' TMD materials.

Computational Tools to Rationalize and Predict the Self-Assembly Behavior of Supramolecular Gels

Supramolecular gels form a class of soft materials that has been heavily explored by the chemical community in the past 20 years. While a multitude of experimental techniques has demonstrated its usefulness when characterizing these materials, the potential value of computational techniques has received much less attention. This review aims to provide a complete overview of studies that employ computational tools to obtain a better fundamental understanding of the self-assembly behavior of supramolecular gels or to accelerate their development by means of prediction. As such, we hope to stimulate researchers to consider using computational tools when investigating these intriguing materials. In the concluding remarks, we address future challenges faced by the field and formulate our vision on how computational methods could help overcoming them.

Pristine graphene covalent functionalization with aromatic aziridines and their application in the sensing of volatile amines - an ab initio investigation

Food quality is of paramount importance for public health safety. For instance, fish freshness can be assessed by sensing the volatile short chain alkylamines produced by spoiled fish. Functionalized graphene is a good candidate for the design of gas sensors for such compounds and therefore of interest as the basic material in food quality sensor devices. To shed theoretical insight in this direction, in the present work we investigate via first-principles density functional theory (DFT) simulations: (i) graphene functionalization via aziridine appendages and (ii) the adsorption of short chain alkylamines (methylamine MA, dimethylamine DMA, and trimethylamine TMA) on the chemically functionalized graphene sheets. Optimal geometries, adsorption energies, and projected density of states (PDOS) are computed using a DFT method. We show that nitrene reactive intermediates, formed by thermal or photo splitting of arylazides - p-carboxyphenyl azide (1a), p-carboxyperfluorophenyl azide (1b), and p-nitrophenyl azide (1c) - react with graphene to yield functionalized derivatives, with reaction energies >-1.0 eV and barriers of the order of 2.0 eV, and open a ∼0.3 to 0.5 eV band gap which is in principle apt for applications in sensing and electronic devices. The interaction between the amines and functionalized graphene, as demonstrated from the calculations of charge density differences showing regions of charge gain and others of charge depletion between the involved groups, occurs through hydrogen bonding with interaction energies ranging from -0.04 eV to -0.76 eV, and induce charge differences in the system, which in the case of p-carboxyperfluorophenyl azide (1b) are sizeable enough to be experimentally observable in sensing.

Quantum Monte Carlo Study of the Water Dimer Binding Energy and Halogen-π Interactions

Halogen-π systems are involved with competition between halogen bonding and π-interaction. Using the diffusion quantum Monte Carlo (DMC) method, we compare the interaction of benzene with diatomic halogens (X₂: Cl₂/Br₂) with the typical hydrogen bonding in the water dimer, taking into account explicit correlations of up to three bodies. The benzene-Cl₂/Br₂ binding energies (13.07 ± 0.42/16.62 ± 0.02 kJ/mol) attributed to both halogen bonding and dispersion are smaller than but comparable to the typical hydrogen bonding in the water dimer binding energy (20.88 ± 0.27 kJ/mol). All of the above values are in good agreement with those from the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)) results at the complete basis set limit (benzene-Cl₂/Br₂: 12.78/16.17 kJ/mol; water dimer: 21.0 kJ/mol).

Thermally and Magnetically Robust Triplet Ground State Diradical

High spin ( S = 1) organic diradicals may offer enhanced properties with respect to several emerging technologies, but typically exhibit low singlet triplet energy gaps and possess limited thermal stability. We report triplet ground state diradical 2 with a large singlet-triplet energy gap, Δ E_ST ≥ 1.7 kcal mol^-1, leading to nearly exclusive population of triplet ground state at room temperature, and good thermal stability with onset of decomposition at ∼160 °C under inert atmosphere. Magnetic properties of 2 and the previously prepared diradical 1 are characterized by SQUID magnetometry of polycrystalline powders, in polystyrene glass, and in other matrices. Polycrystalline diradical 2 forms a novel one-dimensional (1D) spin-1 ( S = 1) chain of organic radicals with intrachain antiferromagnetic coupling of J'/ k = -14 K, which is associated with the N···N and N···O intermolecular contacts. The intrachain antiferromagnetic coupling in 2 is by far strongest among all studied 1D S = 1 chains of organic radicals, which also makes 1D S = 1 chains of 2 most isotropic, and therefore an excellent system for studies of low-dimensional magnetism. In polystyrene glass and in frozen benzene or dibutyl phthalate solution, both 1 and 2 are monomeric. Diradical 2 is thermally robust and is evaporated under ultrahigh vacuum to form thin films of intact diradicals on silicon substrate, as demonstrated by X-ray photoelectron spectroscopy. Based on C-K NEXAFS spectra and AFM images of the ∼1.5 nm thick films, the diradical molecules form islands on the substrate with molecules stacked approximately along the crystallographic a-axis. The films are stable under ultrahigh vacuum for at least 60 h but show signs of decomposition when exposed to ambient conditions for 7 h.

S = 1 Tetraazacyclophane Diradical Dication with Robust Stability: A Case of Low-Temperature One-Dimensional Antiferromagnetic Chain

One-dimensional (1D) spin-1 ( S = 1) chain of organic radicals with low local magnetic anisotropy may provide a better understanding of the low-dimensional magnetism. We report solid-state studies, including single crystal X-ray crystallography, of air-stable tetraazacyclophane diradical dication salt 1^2·2+·2[Al(OC(CF₃)₂CH₃)₄]^- with a triplet ground state (Δ E_ST ≈ 0.5 kcal mol^-1). The magnetic behavior for 1^2·2+ at low temperature is best modeled by 1D spin S = 1 Heisenberg chain with intrachain antiferromagnetic coupling of J'/ k = -5.4 K, which is associated with the interaryl C···C contacts, including π-π interactions. Zero-field splitting value, | D/ hc| ≈ 5.6 × 10^-3 cm^-1, for 1^2·2+ is rather small; thus, the 1D chains are characterized by the high degree of isotropicity | D/2 J'| ≈ 7.5 × 10^-4. The diradical dication salt possesses extraordinary stability with onset of decomposition at temperature of about 180 °C (∼450 K), based on thermogravimetric analysis and EPR spectroscopy.

Anisotropic and amphoteric characteristics of diverse carbenes

The singlet/triplet stabilities and amphoteric behaviors of diverse carbenes are elucidated with the anisotropic natures of their electron configurations.

Graphene and Graphene Analogs toward Optical, Electronic, Spintronic, Green-Chemical, Energy-Material, Sensing, and Medical Applications

This spotlight discusses intriguing properties and diverse applications of graphene (Gr) and Gr analogs. Gr has brought us two-dimensional (2D) chemistry with its exotic 2D features of density of states. Yet, some of the 2D or 2D-like features can be seen on surfaces and at interfaces of bulk materials. The substrate on Gr and functionalization of Gr (including metal decoration, intercalation, doping, and hybridization) modify the unique 2D features of Gr. Despite abundant literature on physical properties and well-known applications of Gr, spotlight works based on the conceptual understanding of the 2D physical and chemical nature of Gr toward vast-ranging applications are hardly found. Here we focus on applications of Gr, based on conceptual understanding of 2D phenomena toward 2D chemistry. Thus, 2D features, defects, edges, and substrate effects of Gr are discussed first. Then, to pattern Gr electronic circuits, insight into differentiating conducting and nonconducting regions is introduced. By utilizing the unique ballistic electron transport properties and edge spin states of Gr, Gr nanoribbons (GNRs) are exploited for the design of ultrasensitive molecular sensing electronic devices (including molecular fingerprinting) and spintronic devices. The highly stable nature of Gr can be utilized for protection of corrosive metals, moisture-sensitive perovskite solar cells, and highly environment-susceptible topological insulators (TIs). Gr analogs have become new types of 2D materials having novel features such as half-metals, TIs, and nonlinear optical properties. The key insights into the functionalized Gr hybrid materials lead to the applications for not only energy storage and electrochemical catalysis, green chemistry, and electronic/spintronic devices but also biosensing and medical applications. All these topics are discussed here with the focus on conceptual understanding. Further possible applications of Gr, GNRs, and Gr analogs are also addressed in a section on outlook and future challenges.

A theoretical study of complexes between fullerenes and concave receptors with interest in photovoltaics

The proper combination of host and guest allows controlling the stability and charge transfer capability of fullerene–concave receptor complexes.

Halogen-π Interactions between Benzene and X2/CX4 (X = Cl, Br): Assessment of Various Density Functionals with Respect to CCSD(T)

Various types of interactions between halogen (X) and π moiety (X-π interaction) including halogen bonding play important roles in forming the structures of biological, supramolecular, and nanomaterial systems containing halogens and aromatic rings. Furthermore, halogen molecules such as X₂ and CX₄ (X = Cl/Br) can be intercalated in graphite and bilayer graphene for doping and graphene functionalization/modification. Due to the X-π interactions, though recently highly studied, their structures are still hardly predictable. Here, using the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)), the Møller-Plesset second-order perturbation theory (MP2), and various flavors of density functional theory (DFT) methods, we study complexes of benzene (Bz) with halogen-containing molecules X₂ and CX₄ (X = Cl/Br) and analyze various components of the interaction energy using symmetry adapted perturbation theory (SAPT). As for the lowest energy conformers (S1), X₂-Bz is found to have the T-shaped structure where the electropositive X atom-end of X₂ is pointing to the electronegative midpoint of CC bond of the Bz ring, and CX₄-Bz has the stacked structure. In addition to this CX₄-Bz (S1), other low energy conformers of X₂-Bz (S2/S3) and CX₄-Bz (S2) are stabilized primarily by the dispersion interaction, whereas the electrostatic interaction is substantial. Most of the density functionals show noticeable deviations from the CCSD(T) complete basis set (CBS) limit binding energies, especially in the case of strongly halogen-bonded conformers of X₂-Bz (S1), whereas the deviations are relatively small for CX₄-Bz where the dispersion is more important. The halogen bond shows highly anisotropic electron density around halogen atoms and the DFT results are very sensitive to basis set. The unsatisfactory performance of many density functionals could be mainly due to less accurate exchange. This is evidenced from the good performance by the dispersion corrected hybrid and double hybrid functionals. B2GP-PLYP-D3 and PBE0-TS(Tkatchenko-Scheffler)/D3 are well suited to describe the X-π interactions adequately, close to the CCSD(T)/CBS binding energies (within ∼1 kJ/mol). This understanding would be useful to study diverse X-π interaction driven structures such as halogen containing compounds intercalated between 2-dimensional layers.

Using Density Functional Theory To Study Neutral and Ionized Stacked Thymine Dimers

Stacking interactions in thymine dimers are studied with density functional theory. According to our calculations, six dimers of comparable stability can be prepared at low temperature, but dimerization is impossible at room temperature due to the large entropy contribution that accompanies it. Analysis of vibrational anharmonic coupling terms shows that each of the dimers exhibits distinct vibrational dynamics. Properties of electron density in the intermolecular region are used to analyze neutral stacked species and their ionized forms. Bond paths and critical points in the intermolecular region are identified, but a simple relationship between binding energy and total electron density in the intermolecular critical points could not be found due to an uneven electron distribution in the binding region. The reduced density gradient was confirmed to be a useful tool for analysis of weak stacking interactions. Those interactions also affect vertical and adiabatic ionization energies, which are computed to be slightly lower for the dimers compared to the monomer.

Interactions of Molecules with cis and trans Double Bonds: A Theoretical Study of cis- and trans-2-Butene

Noncovalent interactions of cis- and trans-2-butene, as the smallest model systems of molecules with cis and trans double bonds, were studied to find potential differences in interactions of these molecules. The study was performed using quantum chemical methods including very accurate CCSD(T)/CBS method. We studied parallel and displaced parallel interactions in 2-butene dimers, in butane dimers, and between 2-butene and saturated butane. The results show the trend that interactions of 2-butene with butane are the strongest, followed by interactions in butane dimers, whereas the interaction in 2-butene dimers are the weakest. The strongest calculated interaction energy is between trans-2-butene and butane, with a CCSD(T)/CBS energy of -2.80 kcal mol(-1) . Interactions in cis-2-butene dimers are stronger than interactions in trans-2-butene dimers. Interestingly, some of the interactions involving 2-butene are as strong as interactions in a benzene dimer. These insights into interactions of cis- and trans-2-butene can improve understanding of the properties and processes that involve molecules with cis and trans double bonds, such as fatty acids and polymers.

A theoretical study of weak interactions in phenylenediamine homodimer clusters

Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.

Importance of the Electron Correlation and Dispersion Corrections in Calculations Involving Enamines, Hemiaminals, and Aminals. Comparison of B3LYP, M06-2X, MP2, and CCSD Results with Experimental Data

While B3LYP, M06-2X, and MP2 calculations predict the ΔG° values for exchange equilibria between enamines and ketones with similar acceptable accuracy, the M06-2X/6-311+G(d,p) and MP2/6-311+G(d,p) methods are required for enamine formation reactions (for example, for enamine 5a, arising from 3-methylbutanal and pyrrolidine). Stronger disagreement was observed when calculated energies of hemiaminals (N,O-acetals) and aminals (N,N-acetals) were compared with experimental equilibrium constants, which are reported here for the first time. Although it is known that the B3LYP method does not provide a good description of the London dispersion forces, while M06-2X and MP2 may overestimate them, it is shown here how large the gaps are and that at least single-point calculations at the CCSD(T)/6-31+G(d) level should be used for these reaction intermediates; CCSD(T)/6-31+G(d) and CCSD(T)/6-311+G(d,p) calculations afford ΔG° values in some cases quite close to MP2/6-311+G(d,p) while in others closer to M06-2X/6-311+G(d,p). The effect of solvents is similarly predicted by the SMD, CPCM, and IEFPCM approaches (with energy differences below 1 kcal/mol).

Disulfuric acid dissociated by two water molecules: ab initio and density functional theory calculations

We have studied geometries, energies and vibrational spectra of disulfuric acid (H2S2O7) and its anion (HS2O7(-)) hydrated by a few water molecules, using density functional theory (M062X) and ab initio theory (SCS-MP2 and CCSD(T)). The most noteworthy result is found in H2S2O7(H2O)2 in which the lowest energy conformer shows deprotonated H2S2O7. Thus, H2S2O7 requires only two water molecules, the fewest number of water molecules for deprotonation among various hydrated monomeric acids reported so far. Even the second deprotonation of the first deprotonated species HS2O7(-) needs only four water molecules. The deprotonation is supported by vibration spectra, in which acid O-H stretching peaks disappear and specific three O-H stretching peaks for H3O(+) (eigen structure) appear. We have also kept track of variations in several geometrical parameters, atomic charges, and hybrid orbital characters upon addition of water. As the number of water molecules added increases, the S-O bond weakens in the case of H2S2O7, but strengthens in the case of HS2O7(-). It implies that the decomposition leading to H2SO4 and SO3 hardly occurs prior to the 2nd deprotonation at low temperatures.

Structural stability, vibrational, and bonding properties of potassium 1, 1'-dinitroamino-5, 5'-bistetrazolate: An emerging green primary explosive

Potassium 1,1'-dinitroamino-5,5'-bistetrazolate (K2DNABT) is a nitrogen rich (50.3% by weight, K2C2N12O4) green primary explosive with high performance characteristics, namely, velocity of detonation (D = 8.33 km/s), detonation pressure (P = 31.7 GPa), and fast initiating power to replace existing toxic primaries. In the present work, we report density functional theory (DFT) calculations on structural, equation of state, vibrational spectra, electronic structure, and absorption spectra of K2DNABT. We have discussed the influence of weak dispersive interactions on structural and vibrational properties through the DFT-D2 method. We find anisotropic compressibility behavior (b<a<c) from pressure dependent structural properties. The predicted equilibrium bulk modulus reveals that K2DNABT is softer than toxic lead azide and harder than the most sensitive cyanuric triazide. A complete assignment of all the vibrational modes has been made and compared with the available experimental results. The calculated zone center IR and Raman frequencies show a blue-shift which leads to a hardening of the lattice upon compression. In addition, we have also calculated the electronic structure and absorption spectra using recently developed Tran Blaha-modified Becke Johnson potential. It is found that K2DNABT is a direct band gap insulator with a band gap of 3.87 eV and the top of the valence band is mainly dominated by 2p-states of oxygen and nitrogen atoms. K2DNABT exhibits mixed ionic (between potassium and tetrazolate ions) and covalent character within tetrazolate molecule. The presence of ionic bonding suggests that the investigated compound is relatively stable and insensitive than covalent primaries. From the calculated absorption spectra, the material is found to decompose under ultra-violet light irradiation.

London dispersion in molecular chemistry--reconsidering steric effects

London dispersion, which constitutes the attractive part of the famous van der Waals potential, has long been underappreciated in molecular chemistry as an important element of structural stability, and thus affects chemical reactivity and catalysis. This negligence is due to the common notion that dispersion is weak, which is only true for one pair of interacting atoms. For increasingly larger structures, the overall dispersion contribution grows rapidly and can amount to tens of kcal mol(-1) . This Review collects and emphasizes the importance of inter- and intramolecular dispersion for molecules consisting mostly of first row atoms. The synergy of experiment and theory has now reached a stage where dispersion effects can be examined in fine detail. This forces us to reconsider our perception of steric hindrance and stereoelectronic effects. The quantitation of dispersion energy donors will improve our ability to design sophisticated molecular structures and much better catalysts.

Benchmark calculations of the adsorption of aromatic molecules on graphene

Selecting the saturated graphene fragment as a model of graphene, we have investigated seven popular density functionals, including ωB97X-D, B97-D, B-LYP-D3, M05-2X, M06-2X, M11-L, and N12, for their performance in describing the adsorption of aromatic molecules on graphene. The best performing functionals are B97-D, B-LYP-D3, and ωB97X-D. M05-2X, M06-2X, and M11-L significantly underestimate the adsorption strengths, while N12 fails completely in this respect. The effects of the basis sets and size of the saturated graphene fragments on the geometries, energies, and properties for the adsorption of aromatic molecules on graphene have also been studied. It was found that the small basis sets such as 6-31G(d) and jun-cc-pVDZ are not suitable for the accurate description of the adsorption of aromatic molecules on graphene. The size of selected graphene fragments has a little effect on both the ωB97X-D and SCS-SAPT0 interaction energies, but the effects of the size of selected graphene fragments on the energy components are significant in some cases of the adsorption of aromatic molecules on graphene. The surprising weakness of electrostatic interactions by F substitution for the adsorption of F-substituted benzenes on graphene was explained using the energy component analysis.

Substituent Effects in π-Stacking of Histidine on Functionalized-SWNT and Graphene

Adsorptions of histidine on the functionalized (10,0) single-walled carbon nanotube (SWNT) and graphene were investigated using density function theory methods, M05-2x and DFT-D. The results show that the binding of the histidine ring to the functionalized SWNT is weaker than that to the pristine SWNT for both singlet and triplet complexes, regardless of the electron-donating (-OH, -NH₂) or electron-withdrawing (-COOH) character and their attached sites. The present decreased binding is opposite to the well-known enhanced binding in the substituted benzene dimers. Since the atoms of the histidine are distant from the substituent atoms by over 6Å, there would be no direct interaction between histidine and the substituent as in the case of the substituted benzene systems. The decreased binding can be mainly driven by the aromaticity of the functionalized SWNT. The nucleus-independent chemical shift (NICS) index analysis for the functionalized SWNTs in deed shows that local aromaticity of SWNT is decreased because of the electron redistribution induced by functional groups, and the π-π stacking between the histidine ring and functionalized-SWNT is therefore decreased as compared to the pristine SWNT. However, the above trend does not remain for the binding between the histidine and graphene. The binding of the histidine to the functionalized graphene with -OH and -NH₂ is just slightly weaker than that to the pristine graphene, while its binding to COOH-SWNT becomes a little bit stronger.

Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives

Fluorographene (FG) is a two-dimensional graphene derivative with promising application potential; however, its reactivity is not understood. We have systematically explored its reactivity in vacuum and polar environments. The C-F bond dissociation energies for homo- and heterolytic cleavage are above 100 kcal/mol, but the barrier of SN2 substitution is significantly lower. For example, the experimentally determined activation barrier of the FG reaction with NaOH in acetone equals 14 ± 5 kcal/mol. The considerable reactivity of FG indicates that it is a viable precursor for the synthesis of graphene derivatives and cannot be regarded as a chemical counterpart of Teflon.

One-pot synthesis of functionalized 4-hydroxy-3-thiomethylcoumarins: detection and discrimination of Co2+ and Ni2+ ions

A variety of 4-hydroxy-3-thiomethylcoumarin derivatives were synthesized via a one-pot three-component reaction catalysed by l-proline at room temperature. One of the derivative was used as fluorescence probe to monitor and distinguish Co²⁺ and Ni²⁺.

Using dispersion-corrected density functional theory to understand supramolecular binding thermodynamics

A recently published theoretical approach employing a nondynamic structure model using dispersion-corrected density functional theory (DFT-D3) to calculate equilibrium free energies of association (Chem. – Eur. J., 2012, 18, 9955–9964) is illustrated by its application to eight supramolecular complexes.

Interactions of CO2with various functional molecules

We report the CO₂-interactions with diverse functional molecules. Useful functional molecules such as melamine showing very large adsorption enthalpy for CO₂are reported.