Density functional theory with London dispersion corrections

Stay Hydrated! Impact of Solvation Phenomena on the CO2 Reduction Reaction at Pb(100) and Ag(100) surfaces

Herein, a comprehensive computational study of the impact of solvation on the reduction reaction of CO2 to formic acid (HCOOH) and carbon monoxide on Pb(100) and Ag(100) surfaces is presented. Results further the understanding of how solvation phenomena influence the adsorption energies of reaction intermediates. We applied an explicit solvation scheme harnessing a combined density functional theory (DFT)/microkinetic modeling approach for the CO2 reduction reaction. This approach reveals high selectivities for CO formation at Ag and HCOOH formation on Pb, resolving the prior disparity between ab initio calculations and experimental observations. Furthermore, the detailed analysis of adsorption energies of relevant reaction intermediates shows that the total number of hydrogen bonds formed by HCOO plays a primary role for the adsorption strength of intermediates and the electrocatalytic activity. Results emphasize the importance of explicit solvation for adsorption and electrochemical reaction phenomena on metal surfaces.

Cytochrome P450 Mediated Cyclization in Eunicellane Derived Diterpenoid Biosynthesis

Terpene cyclization, one of the most complex chemical reactions in nature, is generally catalyzed by two classes of terpene cyclases (TCs). Cytochrome P450s that act as unexpected TC-like enzymes are known but are very rare. In this study, we genome-mined a cryptic bacterial terpenoid gene cluster, named ari, from the thermophilic actinomycete strain Amycolatopsis arida. By employing a heterologous production system, we isolated and characterized three highly oxidized eunicellane derived diterpenoids, aridacins A-C (1-3), that possess a 6/7/5-fused tricyclic scaffold. In vivo and in vitro experiments systematically established a noncanonical two-step biosynthetic pathway for diterpene skeleton formation. First, a class I TC (AriE) cyclizes geranylgeranyl diphosphate (GGPP) into a 6/10-fused bicyclic cis-eunicellane skeleton. Next, a cytochrome P450 (AriF) catalyzes cyclization of the eunicellane skeleton into the 6/7/5-fused tricyclic scaffold through C2-C6 bond formation. Based on the results of quantum chemical computations, hydrogen abstraction followed by electron transfer coupled to barrierless carbocation ring closure is shown to be a viable mechanism for AriF-mediated cyclization. The biosynthetic logic of skeleton construction in the aridacins is unprecedented, expanding the catalytic capacity and diversity of P450s and setting the stage to investigate the inherent principles of carbocation generation by P450s in the biosynthesis of terpenoids.

Pd-Catalyzed Tandem Pathway for Stereoselective Synthesis of (E)-1,3-Enyne from β-Nitroalkenes by Using a Sacrificial Directing Group

The involvement of nitroalkenes instead of minimal one alkyne motif for (E)-1,3-enynes synthesis through a palladium catalyzed stereoselective bond forming pathway at room temperature is presented. Implication of nitro group as a sacrificial directing group, formation of magical alkyne on a newly developed Csp 3 -Csp 3 bond with initial palladium-MBH adduct make this methodology distinctive. This protocol features an unprecedented sequential acetate addition, carbon-carbon bond formation, isomerization of double bond and nitromethane degradation in a tandem catalytic walk via dancing hybridization. Mechanistic understanding through identification of intermediates and computational calculations furnishes complete insight into the tandem catalytic pathway. Broad substrates scope and functional groups tolerance make this synthetic methodology magnificent and dynamic. This represents the first example of stereoselective 1,3-enyne synthesis exclusively from alkene substrates by introducing the concept of sacrificial directing group.

Storage and Diffusion of Carbon Dioxide in the Metal Organic Framework MOF-5─A Semi-empirical Molecular Dynamics Study

Metal-organic frameworks (MOFs) have attracted increasing attention due to their high porosity for exceptional gas storage applications. MOF-5 belongs to the family of isoreticular MOFs (IRMOFs) and consists of Zn4O6+ clusters linked by 1,4-benzenedicarboxylate. Due to the large number of atoms in the unit cell, molecular dynamics simulation based on density functional theory has proved to be too demanding, while force field models are often inadequate to model complex host-guest interactions. To overcome this limitation, an alternative semi-empirical approach using a set of approximations and extensive parametrization of interactions called density functional tight binding (DFTB) was applied in this work to study CO2 in the MOF-5 host. Calculations of pristine MOF-5 yield very good agreement with experimental data in terms of X-ray diffraction patterns as well as mechanical properties, such as the negative thermal expansion coefficient and the bulk modulus. In addition, different loadings of CO2 were introduced, and the associated self-diffusion coefficients and activation energies were investigated. The results show very good agreement with those of other experimental and theoretical investigations. This study provides detailed insights into the capability of semi-empirical DFTB-based molecular dynamics simulations of these challenging guest@host systems. Based on the comparison of the guest-guest pair distributions observed inside the MOF host and the corresponding gas-phase reference, a liquid-like structure of CO2 can be deduced upon storage in the host material.

Revisiting conventional noncovalent interactions towards a complete understanding: from tetrel to pnicogen, chalcogen, and halogen bond

Typical noncovalent interactions, including tetrel (TtB), pnicogen (PniB), chalcogen (ChalB), and halogen bonds (HalB), were systematically re-investigated by modeling the N⋯Z interactions (Z = Si, P, S, Cl) between NH3 - as a nucleophilic, and SiF4, PF3, SF2, and ClF - as electrophilic components, employing highly reliable ab initio methods. The characteristics of N⋯Z interactions when Z goes from Si to Cl, were examined through their changes in stability, vibrational spectroscopy, electron density, and natural orbital analyses. The binding energies of these complexes at CCSD(T)/CBS indicate that NH3 tends to hold tightly most with ClF (-34.7 kJ mol-1) and SiF4 (-23.7 kJ mol-1) to form N⋯Cl HalB and N⋯Si TtB, respectively. Remarkably, the interaction energies obtained from various approaches imply that the strength of these noncovalent interactions follows the order: N⋯Si TtB > N⋯Cl HalB > N⋯S ChalB > N⋯P PniB, that differs the order of their corresponding complex stability. The conventional N⋯Z noncovalent interactions are characterized by the local vibrational frequencies of 351, 126, 167, and 261 cm-1 for TtB, PniB, ChalB, and HalB, respectively. The SAPT2+(3)dMP2 calculations demonstrate that the primary force controlling their strength retains the electrostatic term. Accompanied by the stronger strength of N⋯Si TtB and N⋯Cl HalB, the AIM and NBO results state that they are partly covalent in nature with amounts of 18.57% and 27.53%, respectively. Among various analysis approaches, the force constant of the local N⋯Z stretching vibration is shown to be most accurate in describing the noncovalent interactions.

2D-2D Nanoheterostructure of an Exposed {001}-Facet CuO and MoS2 Based Bifunctional Catalyst Showing Excellent Surface Chemistry and Conductivity for Cathodic CO2 Reduction

A novel CuO-MoS2 based heterostructure catalyst model system is proposed where a CuO nanosheet with exposed {001} facet with proper termination is the active surface for the catalysis and a MoS2 nanosheet is the supporting layer. Density functional theory (DFT) calculations were performed to validate the model. The MoS2 bilayer forms a stable heterostructure with {001} faceted CuO with different terminations exposing oxygen and copper atoms (active sites) on the surface. The heterostructure active sites with a low oxidation state of the copper atoms and subsurface oxygen atoms provide a suitable chemical environment for the selective production of multicarbon products from CO2 electrocatalytic reduction. Furthermore, our heterostructure model exhibits good electrical conductivity, efficient electron transport to active surface sites, and less interfacial resistance compared to similar heterostructure systems. Additionally, we propose a photoenhanced electrocatalysis mechanism due to the photoactive nature of MoS2. We suggest that the photogenerated carrier separation occurs because of the interface-induced dipole. Moreover, we utilized a machine learning model trained on a 2D DFT materials database to predict selected properties and compared them with the DFT results. Overall, our study provides insights into the structure-property relationship of a MoS2 supported 2D CuO nanosheet based bifunctional catalyst and highlights the advantages of heterostructure formation with selective morphology and properly terminated surface in tuning the catalytic performance of nanocomposite materials.

Net Intermolecular Silyloxypyrone-Based (5+2) Cycloadditions Utilizing Amides as Enabling and Cleavable Tethers

Silyloxypyrone-based (5+2) cycloadditions were facilitated by amides that allowed for increased reactivity and a pathway for cleaving the tether to afford net intermolecular cycloadducts. Various amides underwent facile cycloaddition, and several experiments revealed steric and electronic factors that accelerate the reaction. tert-Butyl amides reacted faster than less hindered variants in multiple cases. In the case of dearomative oxidopyrylium-indole (5+2) cycloadditions, an amine-based tether was ineffective, whereas amides enabled this powerful transformation. Theoretical calculations evidenced a concerted asynchronous reaction in which the amide facilitates a conformational driving force enabling cycloaddition. Finally, a one-pot acylation/(5+2) cycloaddition/nucleophilic lactam opening and other examples of tosyl lactam opening of a modified cycloadduct were demonstrated.

The Role of Water in the Adsorption of Nitro-Organic Pollutants on Activated Carbon

The density functional theory (DFT) is applied to theoretically study the capture and storage of three different nitro polycyclic aromatic hydrocarbons, 4-nitrophenol, 2-nitrophenol, and 9-nitroanthracene by activated carbon, with and without the presence of water. These species are pollutants derived from vehicle and industry emissions. The modeling of adsorption is carried out at the molecular level using a high-level density functional theory with the B3LYP-GD(BJ)/6-31+G(d,p) level of theory. The adsorption energies of polluting gases considered isolated and in a humid environment are compared to better understand the role of water. The calculations reveal different possible pathways involving the formation of chemical bonds between adsorbent and adsorbate on the formation of intermolecular van der Waals interactions. The negative adsorption energy on AC for the three species is obtained when they are treated individually and in mixture with H2O. The basis-set superposition error, estimated using the counterpoise correction, varies the adsorption energies by 2-13%. Dispersion effects were also taken into account. The adsorption energy ranges from -10 to -414 kJ/mol suggesting a diversity of pathways. The resulting analysis suggests three preferred pathways for capture. The main pathway is physical interaction due to π-π stacking. Other means are capture due to the formation of hydrogen bonds resulting from water adsorbed on the surface and the simultaneous adsorption of pollutant and water where water can act as a link that promotes adsorption. The thermodynamic properties give a clue to the most eco-friendly approaches for molecular adsorption.

Seven new secondary metabolites isolated from roots of Lespedeza bicolor

Chemical investigation of a methanol extract obtained from the roots of Lespedeza bicolor identified one new pterocarpene (1), three new pterocarpans (2-4), and three new arylbenzofurans (5-7), and two known compounds (8 and 9). Their structures were determined by interpretations obtained from combined UV, NMR, and HRTOFMS spectroscopic data. Furthermore, the absolute configurations of compounds 2 and 3 were established by the combination of electronic circular dichroism (ECD) calculations and NMR calculations with DP4+ probability analysis. All isolated compounds (1-9) were evaluated for cytotoxicity against the human lung carcinoma cell line A549 and the human hepatoma cell line Huh-7. Compound 4 showed antiproliferative activity against A549 cell line with IC50 value of 24.9 μM. Furthermore, compound 9 exhibited cytotoxicity against Huh-7 cell line with IC50 value of 68.7 μM.

Conformational Effect on the Excitonic States of 2-Phenylpyridine Oligomers: Ab Initio Studies and Analysis

In this work, we report the effect of different conformations of 2-phenylpyridine oligomers ((PhPy)n=1-5) on the excited state properties from the results obtained at the RI-ADC(2)/def2-TZVP level. Three different conformers, namely, A, B, and C, are considered for each oligomer. All the oligomers of conformer A have linear-type structures, whereas conformers B and C form helical structures at n = 5 and n = 3, respectively. The differences in the geometries of the three conformers are reflected in the UV and CD spectra. The UV spectra of conformer A show high-intensity peaks compared to the conformers B and C, for each oligomer. While the helical oligomers of conformers B and C show high-intensity CD bands, the intensities of CD bands for all of the oligomers of conformer A are weaker. Analysis of the properties of the first five excited states in (PhPy)5 is carried out using three descriptors, and the results reveal that these are partially charge transfer states.

Theoretical investigation of anion perfluorocubane

CONTEXT

In this work, we did a theoretical exploration of C8F8 (Ib) and its anion radical analogue (IIb) in this work. By investigating the thermochemistry of electron capture, we find that the free energy associated with the conversion of C8H8 (Ia) into its anion radical analogue IIa is of the order of + 92.83 kcal.mol-1, while the conversion of Ib into IIb is - 6.42 kcal.mol-1. Therefore, species IIb is thermodynamically more stable than its neutral analogue. Natural bond orbitals (NBO) analyses revealed that compound Ib exhibits a relative electronic stability as a function of intramolecular delocalisations of the type [Formula: see text] of the order of 2.70 kcal.mol-1. Similar delocalizations for Ia are energetically lower (1.45 kcal.mol-1). Topological analyses of compounds Ib and IIb indicate that the addition of an electron to Ib enhances the covalency of the C-C bond, as can be seen by the reduction in the ellipticity of the C-C bond. The opposite is observed for Ia, whose addition of the electron (leading to IIa) reduces the covalency of the C-C bond. By comparing the free and packaged forms of the species, it is found that, in the crystalline form, the system will present greater relative stability due to the dispersive interactions involved, as evidenced by non-covalent interactions (NCI) analysis. Finally, it was possible to verify that the manifestation of the current density with a lower paratropic and less antiaromatic character in Ib and IIb point to C8F8 as a strong candidate for electron capture.

METHODS

Geometry optimization calculations were carried out, for all monomer structures using the hybrid functional B3LYP-D3 and the 6-31+G(d,p) basis set. To determine the formation thermochemistry of the ions, electronic energy corrections was performed using the DLPNO-CCSD(T)/aug-cc-pVTZ/C method. Starting from the optimised forms, shielding, nuclear magnetic resonance (NMR) spectra employing gauge-independent atomic orbital (GIAO), and NBO calculations were performed for these monomers, using the PBE0 functional and the pCSseg-2 atomic basis set. The magnetochemical analysis of ring currents was performed using the GIMIC formalism. For the topological analysis, it was applied the combination DLPNO-CCSD(T)/aug-cc-pVTZ/C, previously used for correcting the electronic energy.

Study on Asymmetric Vibrational Coherent Magnetic Transitions and Origin of Fluorescence in Symmetric Structures

In this work, the physical mechanisms of three highly efficient circularly polarized luminescent materials are introduced. The UV-vis spectra are plotted; the transition properties of their electrons at the excited states are investigated using a combination of the transition density matrix (TDM) and the charge difference density (CDD); combining the distribution of electron clouds, the essence of charge transfer excitation in three structures is explained. The resonance Raman spectrum of the three structures at the S1 and S2 excited states are calculated. The M, M-4 and M, M-5 structures are found to produce novel chirality by electronic circular dichroism (ECD) spectrum, and the reasons for the chirality of the M, M-4 and M, M-5 structures are discussed by analyzing the density of transition electric/magnetic dipole moments (TEDM/TMDMs) in different orientations. Finally, the Raman optical activity (ROA) of M, M-4, and M, M-5 are calculated, and the spectra are plotted. This study will provide guidance for the application of carbon-based nanomaterials in organic electronic devices, solar cells, and optoelectronics.

Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B12 Derivatives?

Aryl corrins represent a novel class of designed B12 derivatives with biological properties of "antivitamins B12". In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born-Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both "static" DFT calculations and "dynamic" BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made.

CCSD(T) Rotational Constants for Highly Challenging C5H2 Isomers-A Comparison between Theory and Experiment

We evaluate the accuracy of CCSD(T) and density functional theory (DFT) methods for the calculation of equilibrium rotational constants (Ae, Be, and Ce) for four experimentally detected low-lying C5H2 isomers (ethynylcyclopropenylidene (2), pentatetraenylidene (3), ethynylpropadienylidene (5), and 2-cyclopropen-1-ylidenethenylidene (8)). The calculated rotational constants are compared to semi-experimental rotational constants obtained by converting the vibrationally averaged experimental rotational constants (A0, B0, and C0) to equilibrium values by subtracting the vibrational contributions (calculated at the B3LYP/jun-cc-pVTZ level of the theory). The considered isomers are closed-shell carbenes, with cumulene, acetylene, or strained cyclopropene moieties, and are therefore highly challenging from an electronic structure point of view. We consider both frozen-core and all-electron CCSD(T) calculations, as well as a range of DFT methods. We find that calculating the equilibrium rotational constants of these C5H2 isomers is a difficult task, even at the CCSD(T) level. For example, at the all-electron CCSD(T)/cc-pwCVTZ level of the theory, we obtain percentage errors ≤0.4% (Ce of isomer 3, Be and Ce of isomer 5, and Be of isomer 8) and 0.9-1.5% (Be and Ce of isomer 2, Ae of isomer 5, and Ce of isomer 8), whereas for the Ae rotational constant of isomers 2 and 8 and Be rotational constant of isomer 3, high percentage errors above 3% are obtained. These results highlight the challenges associated with calculating accurate rotational constants for isomers with highly challenging electronic structures, which is further complicated by the need to convert vibrationally averaged experimental rotational constants to equilibrium values. We use our best CCSD(T) rotational constants (namely, ae-CCSD(T)/cc-pwCVTZ for isomers 2 and 5, and ae-CCSD(T)/cc-pCVQZ for isomers 3 and 8) to evaluate the performance of DFT methods across the rungs of Jacob's Ladder. We find that the considered pure functionals (BLYP-D3BJ, PBE-D3BJ, and TPSS-D3BJ) perform significantly better than the global and range-separated hybrid functionals. The double-hybrid DSD-PBEP86-D3BJ method shows the best overall performance, with percentage errors below 0.5% in nearly all cases.

A Theoretical Investigation of Novel Sila- and Germa-Spirocyclic Imines and Their Relevance for Electron-Transporting Materials and Drug Discovery

A new class of spirocyclic imines (SCIs) has been theoretically investigated by applying a variety of quantum chemical methods and basis sets. The uniqueness of these compounds is depicted by various peculiarities, e.g., the incidence of planar six-membered rings each with two imine groups (two π bonds) and the incorporation of the isosteres carbon, silicon, or germanium spiro centers. Additional peculiarities of these novel SCIs are mirrored by their three-dimensionality, the simultaneous occurrence of nucleophilic and electrophilic centers, and the cross-hyperconjugative (spiro-conjugation) interactions, which provoke charge mobility along the spirocyclic scaffold. Substitution of SCIs with strong electron-withdrawing substituents, like the cyano group or fluorine, enhances their docking capability and impacts their reactivity and charge mobility. To gain thorough knowledge about the molecular properties of these SCIs, their structures have been optimized and various quantum chemical concepts and models were applied, e.g., full NBO analysis and the frontier molecular orbitals (FMOs) theory (HOMO-LUMO energy gap) and the chemical reactivity descriptors derived from them. For the assessment of the charge density distribution along the SCI framework, additional complementary quantum chemical methods were used, e.g., molecular electrostatic potential (MESP) and Bader's QTAIM. Additionally, using the aromaticity index NICS (nuclear independent chemical shift) and other criteria, it could be shown that the investigated cross-hyperconjugated sila and germa SCIs are spiro-aromatics of the Heilbronner Craig-type Möbius aromaticity.

Unraveling the Pivotal Roles of Various Metal Ion Centers in the Catalysis of Quercetin 2,4-Dioxygenases

Quercetin 2,4-dioxygenase (QueD) with various transition metal ion co-factors shows great differences, but the internal reasons have not been illustrated in detail. In order to explore the effects of metal ion centers on the catalytic reactivity of QueD, we calculated and compared the minimum energy crossing point (MECP) of dioxygen from the relatively stable triplet state to the active singlet state under different conditions by using the DFT method. It was found that the metal ions play a more important role in the activation of dioxygen compared with the substrate and the protein environment. Simultaneously, the catalytic reactions of the bacterial QueDs containing six different transition metal ions were studied by the QM/MM approach, and we finally obtained the reactivity sequence of metal ions, Ni2+ > Co2+ > Zn2+ > Mn2+ > Fe2+ > Cu2+, which is basically consistent with the previous experimental results. Our calculation results indicate that metal ions act as Lewis acids in the reaction to stabilize the substrate anion and the subsequent superoxo and peroxo species in the reaction, and promote the proton coupled electron transfer (PCET) process. Furthermore, the coordination tendencies of transition metal ion centers also have important effects on the catalytic cycle. These findings have general implications on metalloenzymes, which can expand our understanding on how various metal ions play their key role in modulating catalytic reactivity.

Crystal Facet Structure Dependence and Promising Pd-Pt Catalytic Materials for Perhydroacenaphthene Dehydrogenation

Designing an effective Pd-Pt catalytic material with excellent catalytic performance for perhydroacenaphthene (PHAN) dehydrogenation is a great challenge. In this work, in order to explore the crystal facet structure over the bimetallic Pd-Pt catalyst on the dehydrogenation performance of PHAN, the surface compositions of two kinds of Pd (Pt) atoms with different coverage on Pd modulated Pt (PdPt) and Pt modulated Pd (PtPd) catalysts were designed and studied by means of density functional theory (DFT). Through the investigation of the reaction path of PHAN dehydrogenation on PdMLPt(111) and PtMLPd(111) surfaces, it was found that PdMLPt(111) was advantageous to PHAN dehydrogenation (Ea = 2.317 eV). This was attributed to a lower energy barrier, more stable dehydrogenation products, and the fact that Pd doping brought Pt(111) close to the Fermi level. Apparently, Pd modulated Pt catalyst has a broad application prospect in the dehydrogenation of PHAN. In the process of optimizing the PdPt morphology, a method for selecting the minimum active unit of PdPt catalysts with different ratios was proposed, that is, the most stable active unit: rhombus structure was determined according to the surface formation energy. Moreover, we correlated the relationship among the number of H atoms removed, adsorption energy, surface charge, activation energy, reaction energy, and surface coverage, and obtained the important parameters to predict the performance of PdPt catalyst in PHAN dehydrogenation system: surface charge and d-band center. Finally, the essential correlativity among Pd-Pt surface characteristics, catalytic PHAN activity, and adsorption energy was constructed; that is, the relationship model among d-band center, H atom, and product C12H8 adsorption energy was established. This work opens a new simultaneous path to improve the catalytic performance of Pd-Pt-based catalytic materials for PHAN dehydrogenation, which can be achieved by regulating the rhombic active units of Pt modulated by Pd.

Reversible and irreversible stimuli-responsive chromism of a square-planar platinum(ii) salt

A new simple Pt(ii) terpyridyl salt that shows reversible response towards acetonitrile and irreversible response towards methanol has been reported, accompanied with the colorimetric/luminescent changing from red to yellow. Experimentally and theoretically, the spectroscopic change derives from the hydrogen bonds between crystal water in the Pt(ii) terpyridyl salt and external organic molecules, and the different strength of hydrogen bond leads either reversible or irreversible stimuli-response. Furthermore, this Pt(ii) terpyridyl salt has been on one hand applied as a probe for sensing acetonitrile in water solution, with high selectivity, good reversibility, proper sensitivity and fast response rate, and on the other hand as advanced anticounterfeiting materials. The current study provides a new approach to acquire and design either reversible or irreversible stimuli-responsive luminescent materials.

Fine-Tuning the Molecular Design for High-Performance Molecular Diodes Based on Pyridyl Isomers

Better control of molecule-electrode coupling (Γ) to minimize leakage current is an effective method to optimize the functionality of molecular diodes. Herein we embedded 5 isomers of phenypyridyl derivatives, each with an N atom placed at a different position, in two electrodes to fine-tune Γ between self-assembled monolayers (SAMs) and the top electrode of EGaIn (eutectic Ga-In terminating in Ga2 O3 ). Combined with electrical tunnelling results, characterizations of electronic structures, single-level model fittings, and DFT calculations, we found that the values of Γ of SAMs formed by these isomers could be regulated by nearly 10 times, thereby contributing to the leakage current changing over about two orders of magnitude and switching the isomers from resistors to diodes with a rectification ratio (r+ =|J(+1.5 V)/J(-1.5 V)|) exceeding 200. We demonstrated that the N atom placement can be chemically engineered to tune the resistive and rectifying properties of the molecular junctions, making it possible to convert molecular resistors into rectifiers. Our study provides fundamental insights into the role of isomerism in molecular electronics and offers a new avenue for designing functional molecular devices.

Promoting Oxygen Reduction Reaction on Carbon-based Materials by Selective Hydrogen Bonding

Electrochemical oxygen reduction reaction (ORR) is fundamental for many energy conversion and storage devices. Selective tuning of *OOH/*OH adsorption energy to break the intrinsic scaling limitation (ΔG*OOH =ΔG*OH +3.2 eV) is effective in optimizing the ORR limiting potential (UL ), which is practically challenging to achieve by constructing a particular catalyst. Herein, using first-principles calculations, we elucidated how to rationally plant an additional *OH that can selectively interact with the ORR intermediate of *OOH via hydrogen bonding, while not affecting the *OH intermediate. Guided by the design principle, we successfully tailored a series of novel carbon-based catalysts, with merits of low-cost, long-lasting, synthesis feasibility, exhibiting a high UL (1.06 V). Our proposed strategy comes up with a new linear scaling relationship of ΔG*OOH =ΔG*OH +2.84 eV. This approach offers a great possibility for the rational design of efficient catalysts for ORR and other chemical reactions.

Efficient Calculation of the Dispersion Energy for Multireference Systems with Cholesky Decomposition: Application to Excited-State Interactions

Accurate and efficient prediction of dispersion interactions in excited-state complexes poses a challenge due to the complex nature of electron correlation effects that need to be simultaneously considered. We propose an algorithm for computing the dispersion energy in nondegenerate ground- or excited-state complexes with arbitrary spin. The algorithm scales with the fifth power of the system size due to employing Cholesky decomposition of Coulomb integrals and a recently developed recursive formula for density response functions of the monomers. As a numerical illustration, we apply the new algorithm in the framework of multiconfigurational symmetry adapted perturbation theory, SAPT(MC), to study interactions in dimers with localized excitons. The SAPT(MC) analysis reveals that the dispersion energy may be the main force stabilizing excited-state dimers.

Floating in Space: How to Treat the Weak Interaction between CO Molecules in Interstellar Ices

In the interstellar medium, six molecules have been conclusively detected in the solid state in interstellar ices, and a few dozen have been hypothesized and modeled to be present in the solid state as well. The icy mantles covering micrometer-sized dust grains are, in fact, thought to be at the core of complex molecule formation as a consequence of the local high density of molecules that are simultaneously adsorbed. From a structural perspective, the icy mantle is considered to be layered, with an amorphous water-rich inner layer surrounding the dust grain, covered by an amorphous CO-rich outer layer. Moreover, recent studies have suggested that the CO-rich layer might be crystalline and possibly even be segregated as a single crystal atop the ice mantle. If so, there are far-reaching consequences for the formation of more complex organic molecules, such as methanol and sugars, that use CO as a backbone. Validation of these claims requires further investigation, in particular on acquiring atomistic insight into surface processes, such as adsorption, diffusion, and reactivity on CO ices. Here, we present the first detailed computational study toward treating the weak interaction of (pure) CO ices. We provide a benchmark of the performance of various density functional theory methods in treating the binding of pure CO ices. Furthermore, we perform an atomistic and in-depth study of the binding energy of CO on amorphous and crystalline CO ices using a pair-potential-based force field. We find that CO adsorption is represented by a large distribution of binding energies (200-1600 K) on amorphous CO, including a significant amount of weak binding sites (<350 K). Increasing both the cluster size and the number of neighbors increases the mean of the observed binding energy distribution. Finally, we find that CO binding energies are dominated by dispersion and, as such, exchange-correlation functionals need to include a treatment of dispersion to accurately simulate surface processes on CO ices. In particular, we find the ωB97M-V functional to be a strong candidate for such simulations.

London Dispersion Effects on the Stability of Heavy Tetrel Molecules

London dispersion (LD) interactions, which stem from long-range electron correlations arising from instantaneously induced dipoles can occur between neighboring atoms or molecules, for example, between H atoms within ligand C-H groups. These interactions are currently of interest as a new method of stabilizing long bonds and species with unusual oxidation states. They can also limit reactivity by installing LD enhanced groups into organic frameworks or ligand substituents. Here, we address the most recent advances in the design of LD enhanced ligands, the sterically counterintuitive structures that can be generated and the consequences that these interactions can have on the structures and reactivity of sterically crowded heavy group 14 species.

Cl@Si20X20 cages: evaluation of encapsulation nature, structural rigidity, and 29Si-NMR patterns using relativistic DFT calculations

The experimental characterization of Cl@Si₂₀ endohedral clusters, featuring different ligands such as [Cl@Si₂₀H₂₀]^- (1) [Cl@Si₂₀H₁₂Cl₈]^- (2), and [Cl@Si₂₀Cl₂₀]^- (3), provides insight into the variable encapsulation environment for chloride anions. The favorable formation of such species enables the evaluation of the encapsulation nature and the role of the inner anion in the rigidity of the overall cluster. Our results show a sizable interaction which increases as -66.7, -100.8, and -130.3 kcal mol^-1 from 1 to 3, respectively, featuring electrostatic character. The orbital interaction involves 3p-Cl → Si₂₀X₂₀ and 3s-Cl → Si₂₀X₂₀ charge transfer channels and a slight contribution from London dispersion-type interactions. These results show that the inner bonding environment can be modified by the choice of exobonded ligands. Moreover, ²⁹Si-NMR parameters are depicted in terms of the chemical shift anisotropy (CSA), leading to a strong variation of the three principal tensor components (δ₁₁, δ₂₂, δ₃₃), unraveling the origin of the experimental ²⁹Si-NMR chemical shift (δ_iso) differences along the given series. Thus, the Si₂₀ cage is a useful template to further evaluate different environments for encapsulating atomic species.

Core-Projected Hybrids Fix Systematic Errors in Time-Dependent Density Functional Theory Predicted Core-Electron Excitations

Linear response time-dependent density functional theory (TDDFT) is widely applied to valence, Rydberg, and charge-transfer excitations but, in its current form, makes large errors for core-electron excitations. This work demonstrates that the admixture of nonlocal exact exchange in atomic core regions significantly improves TDDFT-predicted core excitations. Exact exchange admixture is accomplished using projected hybrid density functional theory [ J. Chem. Theory Comput. 2023, 19, 837-847]. Scalar relativistic TDDFT calculations using core-projected B3LYP accurately model core excitations of second-period elements C-F and third-period elements Si-Cl, without sacrificing performance for the relative shifts of core excitation energies. Predicted K-edge X-ray near absorption edge structure (XANES) of a series of sulfur standards highlight the value of this approach. Core-projected hybrids appear to be a practical solution to TDDFT's limitations for core excitations, in the way that long-range-corrected hybrids are a practical solution to TDDFT's limitations for Rydberg and charge-transfer excitations.

Evidence for Ruthenium(II) Peralkene Complexes as Catalytic Species during the Isomerization of Terminal Alkenes in Solution

The isomerization (chain-walking) reaction of terminal to internal alkenes is catalyzed by part-per-million amounts of practically any Ru source when the reaction is carried out with a neat terminal alkene. Here, we provide evidence that the soluble starting Ru sources evolve to catalytically active peralkene Ru(II) species under reaction conditions. These species may also explain the isomerization products found during other Ru-catalyzed alkene processes, i.e., alkene metathesis reactions. A Finke-Watzky mechanism for catalyst formation is consistent with the evidence obtained.

Dye spectra of benzene derivatives in the liquid-crystalline phase of 4-n-pentyl-4΄-cyanobiphenyl

In the present paper, we study the interaction of associates (dimers and trimers) of 4-n-pentyl-4΄-cyanobiphenyl (5CB) with 1, 2-Diamino-4-nitrobenzene and N, N-Dimethyl-4-nitrosoaniline dye molecules. The structures of the intermolecular complexes were studied using hybrid functionals of the DFT method M06 and B3LYP with the 6-31 + G (d) basis set. The intermolecular binding energy of dyes with associates depends on the structure of the complexes and is about 5 kcal/mol. Vibrational spectra were calculated for all intermolecular systems. The electronic absorption spectra of dyes are sensitive to the structure of the mesophase. The pattern of the spectrum changes depending on the structure of the complex of the dimer or trimer with the dye molecule. The long-wavelength transition bands are characterized by shifts that are bathochromic for 1, 2-Diamino-4-nitrobenzene and hypsochromic for N, N-Dimethyl-4-nitrosoaniline.

Uncovering the Mechanism of Azepino-Indole Skeleton Formation via Pictet-Spengler Reaction by Strictosidine Synthase: A Quantum Chemical Investigation

Strictosidine synthase (STR) catalyzes the Pictet-Spengler (PS) reaction of tryptamine and secologanin to produce strictosidine. Recent studies demonstrated that the enzyme can also catalyze the reaction of non-natural substrates to form new alkaloid skeletons. For example, the PS condensation of 1H-indole-4-ethanamine with secologanin could be promoted by the STR from Rauvolfia serpentina (RsSTR) to generate a rare class of skeletons with a seven-membered ring, namely azepino-[3,4,5-cd]-indoles, which are precursors for the synthesis of new compounds displaying antimalarial activity. In the present study, the detailed reaction mechanism of RsSTR-catalyzed formation of the rare seven-membered azepino-indole skeleton through the PS reaction was revealed at the atomic level by quantum chemical calculations. The structures of the transition states and intermediates involved in the reaction pathway were optimized, and the energetics of the complete reaction were analyzed. Based on our calculation results, the most likely pathway of the enzyme-catalyzed reaction was determined, and the rate-determining step of the reaction was clarified. The mechanistic details obtained in the present study are important in understanding the promiscuous activity of RsSTR in the formation of the rare azepino-indole skeleton molecule and are also helpful in designing STR enzymes for the synthesis of other new alkaloid skeleton molecules.

Breaking the tert-Butyllithium Contact Ion Pair: A Gateway to Alternate Selectivity in Lithiation Reactions

The effects of Lewis basic phosphoramides on the aggregate structure of t-BuLi have been investigated in detail by NMR and DFT methods. It was determined that hexamethylphosphoramide (HMPA) can shift the equilibrium of t-BuLi to include the triple ion pair (t-Bu-Li-t-Bu)-/HMPA4Li+ which serves as a reservoir for the highly reactive separated ion pair t-Bu-/HMPA4Li+. Because the Li-atom's valences are saturated in this ion pair, the Lewis acidity is significantly decreased; in turn, the basicity is maximized which allowed for the typical directing effects within oxygen heterocycles to be overridden and for remote sp3 C-H bonds to be deprotonated. Furthermore, these newly accessed lithium aggregation states were leveraged to develop a simple γ-lithiation and capture protocol of chromane heterocycles with a variety of alkyl halide electrophiles in good yields.

Soil amended with Algal Biochar Reduces Mobility of deicing salt contaminants in the environment: An atomistic insight

Soil-based filter media in green infrastructure buffers only a minor portion of deicing salt in surface water, allowing most of that to infiltrate into groundwater, thus negatively impacting drinking water and the aquatic ecosystem. The capacity of the filter medium to adsorb and fixate sodium (Na⁺) and chloride (Cl^-) ions has been shown to improve by biochar amendment. The extent of improvement, however, depends on the type and density of functional groups on the biochar surface. Here, we use density functional theory (DFT) and molecular dynamics (MD) simulations to show the merits of biochar grafted by nitrogenous functional groups to adsorb Cl^-. Our group has shown that such functional groups are abundant in biochar made from protein-rich algae feedstock. DFT is used to model algal biochar surface and its possible interactions with Cl^- through two possible mechanisms: direct adsorption and cation (Na⁺)-bridging. Our DFT calculations reveal strong adsorption of Cl^- to the biochar surface through hydrogen bonding and electrostatic attractions between the ions and active sites on biochar. MD results indicate the efficacy of algal biochar in delaying chloride diffusion. This study demonstrates the potential of amending soils with algal biochar as a dual-targeting strategy to sequestrate carbon and prevent deicing salt contaminants from leaching into water bodies.

Activity Origin of the Nickel Cluster on TiC Support for Nonoxidative Methane Conversion

Designing an active and selective catalyst for nonoxidative conversion of methane under mild conditions is critical for natural gas utilization as a chemical feedstock. Here, we demonstrate that the origin of the selective nonoxidative conversion of methane by the titanium carbide supported nickel cluster arises from the formation of a nickel carbide site under the reaction conditions, which could stabilize the CH_x intermediate to facilitate the C-C coupling, but further coking is rather limited. The reaction mechanism reveals that the C₂ products can be formed via a key -CH_x-CH₃ intermediate. In addition, we demonstrate that boration of the nickel cluster site can improve the methane conversion toward C₂ products. That higher activity and selectivity from the moderate rise in d orbital energy levels can therefore be considered as a descriptor of the catalyst effectiveness. These findings provide an understanding of the dynamic behavior of the single nickel cluster toward methane conversion to C₂ products and guidance for their future rational design.

An Expedited Route to Optical and Electronic Properties at Finite Temperature via Unsupervised Learning

Electronic properties and absorption spectra are the grounds to investigate molecular electronic states and their interactions with the environment. Modeling and computations are required for the molecular understanding and design strategies of photo-active materials and sensors. However, the interpretation of such properties demands expensive computations and dealing with the interplay of electronic excited states with the conformational freedom of the chromophores in complex matrices (i.e., solvents, biomolecules, crystals) at finite temperature. Computational protocols combining time dependent density functional theory and ab initio molecular dynamics (MD) have become very powerful in this field, although they require still a large number of computations for a detailed reproduction of electronic properties, such as band shapes. Besides the ongoing research in more traditional computational chemistry fields, data analysis and machine learning methods have been increasingly employed as complementary approaches for efficient data exploration, prediction and model development, starting from the data resulting from MD simulations and electronic structure calculations. In this work, dataset reduction capabilities by unsupervised clustering techniques applied to MD trajectories are proposed and tested for the ab initio modeling of electronic absorption spectra of two challenging case studies: a non-covalent charge-transfer dimer and a ruthenium complex in solution at room temperature. The K-medoids clustering technique is applied and is proven to be able to reduce by ∼100 times the total cost of excited state calculations on an MD sampling with no loss in the accuracy and it also provides an easier understanding of the representative structures (medoids) to be analyzed on the molecular scale.

Understanding Primary Charge Separation in the Heliobacterial Reaction Center

The homodimeric reaction center of heliobacteria retains features of the ancestral reaction center and can thus provide insights into the evolution of photosynthesis. Primary charge separation is expected to proceed in a two-step mechanism along either of the two reaction center branches. We reveal the first charge-separation step from first-principles calculations based on time-dependent density functional theory with an optimally tuned range-separated hybrid and ab initio Born-Oppenheimer molecular dynamics: the electron is most likely localized on the electron transfer cofactor 3 (EC3, OH-chlorophyll a), and the hole on the adjacent EC2. Including substantial parts of the surrounding protein environment into the calculations shows that a distinct structural mechanism is decisive for the relative energetic positioning of the electronic excitations: specific charged amino acids in the vicinity of EC3 lower the energy of charge-transfer excitations and thus facilitate efficient charge separation. These results are discussed considering recent experimental insights.

Modulation of chiral spectral deflection by van der Waals force-induced molecular electropolarization in catenane oligomers

The striking chiral optical properties of carbon nanostructures are closely related to the precise three-dimensional spatial arrangement (interaction) of carbon atoms. This work investigated the chiral optical properties of three different structures of all-benzene catenane and trefoil knot regulated by van der Waals (vdW) forces using density functional theory (DFT) calculations and wave function analysis. We systematically illustrate how molecular electrical polarization modulates the chiral optical deflection of alkane oligomers under the induction of van der Waals forces. In this work, the UV-vis spectra, transition density matrices (TDM), and electron-hole density diagrams of three molecules have been studied. Combined with a visualization method to represent the effect of molecular polarization on transition electric/magnetic dipole moments (TEDMs\TMDMs), the results show that vdW interactions can induce chirality deflection in polymers. This mechanism provides a clear direction for designing polymers with specific chirality: by modifying the structure, vdW interactions can be generated in specific regions, and then the chirality of the molecule can be precisely regulated. This will help us to establish a strategy for precisely-oriented design of chiral optical materials, and provide guidance for the application and development of optoelectronic materials in specific fields.

Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (Mpro) and Papain-like Protease (PLpro)

The SARS-CoV-2 pandemic has prompted global efforts to develop therapeutics. The main protease of SARS-CoV-2 (M^pro) and the papain-like protease (PL^pro) are essential for viral replication and are key targets for therapeutic development. In this work, we investigate the mechanisms of SARS-CoV-2 inhibition by diphenyl diselenide (PhSe)₂ which is an archetypal model of diselenides and a renowned potential therapeutic agent. The in vitro inhibitory concentration of (PhSe)₂ against SARS-CoV-2 in Vero E6 cells falls in the low micromolar range. Molecular dynamics (MD) simulations and density functional theory (DFT) calculations [level of theory: SMD-B3LYP-D3(BJ)/6-311G(d,p), cc-pVTZ] are used to inspect non-covalent inhibition modes of both proteases via π-stacking and the mechanism of covalent (PhSe)₂ + M^pro product formation involving the catalytic residue C145, respectively. The in vitro CC₅₀ (24.61 μM) and EC₅₀ (2.39 μM) data indicate that (PhSe)₂ is a good inhibitor of the SARS-CoV-2 virus replication in a cell culture model. The in silico findings indicate potential mechanisms of proteases' inhibition by (PhSe)₂; in particular, the results of the covalent inhibition here discussed for M^pro, whose thermodynamics is approximatively isoergonic, prompt further investigation in the design of antiviral organodiselenides.

Machine Learning Interatomic Potentials and Long-Range Physics

Advances in machine learned interatomic potentials (MLIPs), such as those using neural networks, have resulted in short-range models that can infer interaction energies with near ab initio accuracy and orders of magnitude reduced computational cost. For many atom systems, including macromolecules, biomolecules, and condensed matter, model accuracy can become reliant on the description of short- and long-range physical interactions. The latter terms can be difficult to incorporate into an MLIP framework. Recent research has produced numerous models with considerations for nonlocal electrostatic and dispersion interactions, leading to a large range of applications that can be addressed using MLIPs. In light of this, we present a Perspective focused on key methodologies and models being used where the presence of nonlocal physics and chemistry are crucial for describing system properties. The strategies covered include MLIPs augmented with dispersion corrections, electrostatics calculated with charges predicted from atomic environment descriptors, the use of self-consistency and message passing iterations to propagated nonlocal system information, and charges obtained via equilibration schemes. We aim to provide a pointed discussion to support the development of machine learning-based interatomic potentials for systems where contributions from only nearsighted terms are deficient.

Metal Atoms (Li, Na, and K) Tuning the Configuration of Pyrrole for the Selective Recognition of C60

Host-guest structure assembly is significant in the recognition of molecules, and the fullerene-based host-guest structure is a convenient method to determine the structures of fullerenes of which recognition is with many difficulties in experiments. Here, with density functional theory calculations, we designed several crown-shaped pyrrole-based hosts tuned by doping metal atoms (Li, Na, and K) for the effective recognition of C₆₀ with modest interaction between the host and guest. Binding energy calculations showed an enhanced interaction of the concave-convex host-guest system with the doped metal atoms, enabling the selective recognition of C₆₀. The electrostatic interaction between the host and guest was studied by the natural bond order charge analysis, reduced density gradient, and electrostatic potential. Furthermore, the UV-vis-NIR spectra of host-guest structures were simulated to give guidance on the release of the fullerene guest. With much expectation, this work would give a new strategy to design new hosts for effectively recognizing much more fullerene molecules with modest interaction and would be useful for the assembly involving fullerenes.

Performance of Density Functionals and Semiempirical 3c Methods for Small Gold-Thiolate Clusters

In light of the recent surge in computational studies of gold thiolate clusters, we present a comparison of popular density functionals (DFAs) and three-part corrected methods (3c-methods) on their performance by taking a data set named as AuSR18 consisting of 18 isomers of Au_n(SCH₃)_m (m ≤ n = 1-3). We have compared the efficiency and accuracy of the DFAs and 3c-methods in geometry optimization with RI-SCS-MP2 as the reference method. Similarly, the performance for accurate and efficient energy evaluation was compared with DLPNO-CCSD(T) as the reference method. The lowest energy structure among the isomers of the largest stoichiometry from our data set, AuSR18, i.e., Au₃(SCH₃)₃, is considered to evaluate the computational time for SCF and gradient evaluations. Alongside this, the numbers of optimization steps to locate the most stable minima of Au₃(SCH₃)₃ are compared to assess the efficiency of the methods. A comparison of relevant bond lengths with the reference geometries was made to estimate the accuracy in geometry optimization. Some methods, such as LC-BLYP, ωB97M-D3BJ, M06-2X, and PBEh-3c, could not locate many of the minima found by most of the other methods; thus, the versatility in locating various minima is also an important criterion in choosing a method for the given project. To determine the accuracy of the methods, we compared the relative energies of the isomers in each stoichiometry and the interaction energy of the gold core with the ligands. The dependence of basis set size and relativistic effects on energies are also compared. The following are some of the highlights. TPSS has shown accuracy, while mPWPW shows comparable speed and accuracy. For the relative energies of the clusters, the hybrid range-separated DFAs are the best option. CAM-B3LYP excels, whereas B3LYP performs poorly. Overall, LC-BLYP is a balanced performer considering both the geometry and relative stability of the structures, but it lacks diversity. The 3c-methods, although fast, are less impressive in relative stability.

Inorganic Drugs as a Tool for Protein Structure Solving and Studies on Conformational Changes

Inorganic drugs are capable of tight interactions with proteins through coordination towards aminoacidic residues, and this feature is recognized as a key aspect for their pharmacological action. However, the "protein metalation process" is exploitable for solving the phase problem and structural resolution. In fact, the use of inorganic drugs bearing specific metal centers and ligands capable to drive the binding towards the desired portions of the protein target could represent a very intriguing and fruitful strategy. In this context, a theoretical approach may further contribute to solve protein structures and their refinement. Here, we delineate the main features of a reliable experimental-theoretical integrated approach, based on the use of metallodrugs, for protein structure solving.

Insights into molecular cluster materials with adamantane-like core structures by considering dimer interactions

A class of adamantane-like molecular materials attracts attention because they exhibit an extreme non-linear optical response and emit a broad white-light spectrum after illumination with a continuous-wave infrared laser source. According to recent studies, not only the nature of the cluster molecules, but also the macroscopic structure of the materials determines their non-linear optical properties. Here we present a systematic study of cluster dimers of the compounds AdR₄ and [(RT)₄ S₆ ] (T = Si, Ge, Sn) with R = methyl, phenyl or 1-naphthyl to gain fundamental knowledge about the interactions in the materials. For all compounds, a similar type of dimer structures with a staggered arrangement of substituents was determined as the energetically most favorable configuration. The binding energy between the dimers, determined by including London dispersion interactions, increases with the size of the core and the substituents. The cluster interactions can be classified as substituent-substituent-dominated (small cores, large substituents) or core-core-dominated (large cores, small substituents). Among various possible dimer conformers, those with small core-core distances are energetically preferred. Trimer and tetramer clusters display similar trends regarding the minimal core-core distances and binding energies. The much lower energy barrier determined for the rotation of substituents as compared to the rotation of the cluster dimers past each other indicates that the rotation of substituents more easily leads to different conformers in the material. Thus, understanding the interaction of the cluster dimers allows an initial assessment of the interactions in the materials.

Visible-Light Promoted Intramolecular para-Cycloadditions on Simple Aromatics

Dearomative cycloadditions are a powerful tool to access a large chemical space exploiting simple and ubiquitous building blocks. The energetic burden due to the loss of aromaticity has however greatly limited their synthetic potential. We devised a general intramolecular method that overcomes these limitations thanks to the photosensitization of allenamides. The visible-light-promoted process gives complex [2.2.2]-(hetero)-bicyclooctadienes at room temperature, likely through the stabilization of transient (bi)radicals by naphthalene. The reaction tolerates several valuable functionalities, offering a convenient handle for a myriad of applications, including original isoindoles and metal complexes.

Computational insights into the reactivity for the [2+5] cycloaddition reactions of norbornene-linked group 14 element/P-based and Si/group 15 element-based frustrated Lewis pairs with benzaldehyde

The element effects of Lewis acid (LA) and Lewis base (LB) on the potential energy surfaces of [2+5] cycloaddition reactions of norbornene-based G14/P-based (G14 = group 14 element) and Si/G15-based (G15 = group 14 element) frustrated Lewis pair (FLP)-type molecules with benzaldehyde were theoretically examined via density functional theory and several sophisticated methods. The theoretical findings indicated that among the above nine norbornene-linked G14/G15-based FLPs, only the Si/N-Rea, Si/P-Rea, and Si/As-Rea FLP-assisted compounds can readily undergo cycloaddition reactions with doubly bonded organic systems from kinetic and thermodynamic viewpoints. The energy decomposition analysis showed that the bonding interactions between the norbornene-based G14/G15-FLPs and benzaldehyde are better described in terms of the singlet-singlet model (donor-acceptor model) rather than the triplet-triplet model (electron-sharing model). In particular, natural orbitals for chemical valence findings revealed that the forward bonding is the lone pair (G15) → p-π*(C) interaction, which is a significantly strong FLP-to-benzaldehyde interaction. However, the back-bonding is the p-π*(G14) ← lone-pair orbital(O) interaction, which is a weak benzaldehyde-to-FLP interaction. The analyses based on the activation strain model showed that the larger the atomic radius of either the G14(LA) or the G15(LB) atom, the greater the G14⋯G15 separation distance in the norbornene-based G14/G15-FLP molecule, the smaller the orbital overlaps between G14/G15-FLP and Ph(H)CO, and the higher the activation barrier during its cycloaddition reaction with benzaldehyde.

Long-range interactions of aromatic molecules with alkali-metal and alkaline-earth-metal atoms

The isotropic and anisotropic coefficients C_n ^l,m of the long-range spherical expansion ∼1/Rⁿ (R-the intermolecular distance) of the dispersion and induction intermolecular energies are calculated using the first principles for the complexes containing an aromatic molecule (benzene, pyridine, furan, and pyrrole) and alkali-metal (Li, Na, K, Rb, and Cs) or alkaline-earth-metal (Be, Mg, Ca, Sr, and Ba) atoms in their electronic ground states. The values of the first- and second-order properties of the aromatic molecules are calculated using the response theory with the asymptotically corrected LPBE0 functional. The second-order properties of the closed-shell alkaline-earth-metal atoms are obtained using the expectation-value coupled cluster theory and of the open-shell alkali-metal atoms using analytical wavefunctions. These properties are used for the calculation of the dispersion C_n,disp ^l,m and induction C_n,ind ^l,m coefficients (C_n ^l,m=C_n,disp ^l,m+C_n,ind ^l,m) with n up to 12 using the available implemented analytical formulas. It is shown that the inclusion of the coefficients with n > 6 is important for reproducing the interaction energy in the van der Waals region at R ≈ 6 Å. The reported long-range potentials should be useful for constructing the analytical potentials valid for the whole intermolecular interaction range, which are needed for spectroscopic and scattering studies.

Molecular dynamics simulation studies of 1,3-dimethyl imidazolium nitrate ionic liquid with water

The fundamental understanding of intermolecular interactions of ionic liquids (ILs) with water is essential in predicting IL-water thermodynamic properties. In this study, intermolecular or noncovalent interactions were studied for 1,3-dimethyl imidazolium [DMIM]⁺ cation and nitrate [NO₃]^- anion with water, employing quantum mechanics and molecular dynamics simulations. Molecular dynamics simulations were performed using a revised multipolar polarizable force field. The effect of water on ionic liquids was evaluated in terms of thermodynamic and dynamic properties. Thermodynamic properties included liquid densities ρ, excess molar volumes ΔV^E, and liquid structures gr. Dynamic properties included self-diffusion coefficients D of mixture constituents as a function of water concentration. The density of ionic liquid-water mixtures monotonically decrease with increasing concentration of water. A negative excess volume was obtained for low and high water concentrations, demonstrating strong intermolecular interactions of water with ionic liquid components. Liquid structures of ionic liquid-water mixtures revealed a tendency for anions to interact with cations at shorter intermolecular distances when the water concentration is increased. Diffusion rates were found to increase for all mixture components with increase in the fraction of water. A significant change in the diffusion rate was found at ∼0.3 weight fraction of water. However, the water self-diffusion coefficient was dominant at all concentrations. The ratio of water/anion and anion/cation self-diffusion coefficients was found to decrease linearly with increasing concentration of water molecules.

Model Chemistry Recommendations for Scaled Harmonic Frequency Calculations: A Benchmark Study

Despite the widespread popularity of scaled harmonic frequency calculations to predict experimental fundamental frequencies in chemistry, sparse benchmarking is available to guide users on the appropriate level of theory and basis set choices (model chemistry) or deep understanding of expected errors. An updated assessment of the best approach for scaling to minimize errors is also overdue. Here, we assess the performance of over 600 popular, contemporary, and robust model chemistries in the calculation of scaled harmonic frequencies, evaluating different scaling factor types and their implications in the scaled harmonic frequencies and model chemistry performance. We can summarize our results into three main findings: (1) Using model-chemistry-specific scaling factors optimized for three different frequency regions (low (<1,000 cm^-1), mid (1,000-2,000 cm^-1), and high (>2,000 cm^-1)) results in substantial improvements in the agreement between the scaled harmonic and experimental frequencies compared to other choices. (2) Larger basis sets and more robust levels of theory generally lead to superior performance; however, the particular model chemistry choice matters and poor choices lead to significantly reduced accuracies. (3) Outliers are expected in routine calculations regardless of the model chemistry choice. Our benchmarking results here do not consider the intensity of vibrational transitions; however, we draw upon previous benchmarking results for dipole moments that highlight the importance of diffuse functions (i.e., augmented basis sets) in high-quality intensity predictions. In terms of specific recommendations, overall, the highest accuracy model chemistries are double-hybrid density functional approximations with a non-Pople augmented triple-ζ basis set, which can produce median frequency errors down to 7.6 cm^-1 (DSD-PBEP86/def2-TZVPD), which is very close to the error in the harmonic approximation, i.e., the anharmonicity error. Double-ζ basis sets should not be used with double-hybrid functionals as there is no improvement compared to hybrid functional results (unlike for double-hybrid triple-ζ model chemistries). Note that 6-311G* and 6-311+G* basis sets perform like a double-ζ basis set for vibrational frequencies. After scaling, all studied hybrid functionals with non-Pople triple-ζ basis sets will produce median errors of less than 15 cm^-1, with the best result of 9.9 cm^-1 with B97-1/def2-TZVPD. Appropriate matching of double-ζ basis sets with hybrid functionals can produce high-quality results, but the precise choice of functional and basis set is more important. The B97-1, TPSS0-D3(BJ), or ωB97X-D hybrid density functionals with 6-31G*, pc-1, or pcseg-1 are recommended for fast routine calculations, all delivering median errors of 11-12 cm^-1. Note that dispersion corrections are not easily available for B97-1; given its strong performance here, we recommend these be added to major programs in coming updates.

Theoretically Revealing the Response of Intermolecular Vibration Energy Transfer and Decomposition Process of the DNTF System to Electric Fields Using Two-Dimensional Infrared Spectra

The external electric field (E-field), which is an important stimulus, can change the decomposition mechanism and sensitivity of energetic materials. As a result, understanding the response of energetic materials to external E-fields is critical for their safe use. Motivated by recent experiments and theories, the two-dimensional infrared (2D IR) spectra of 3,4-bis (3-nitrofurazan-4-yl) furoxan (DNTF), which has a high energy, a low melting point, and comprehensive properties, were theoretically investigated. Cross-peaks were observed in 2D IR spectra under different E-fields, which demonstrated an intermolecular vibration energy transfer; the furazan ring vibration was found to play an important role in the analysis of vibration energy distribution and was extended over several DNTF molecules. Measurements of the non-covalent interactions, with the support of the 2D IR spectra, indicated that there were obvious non-covalent interactions among different DNTF molecules, which resulted from the conjugation of the furoxan ring and the furazan ring; the direction of the E-field also had a significant influence on the strength of the weak interactions. Furthermore, the calculation of the Laplacian bond order, which characterized the C-NO₂ bonds as trigger bonds, predicted that the E-fields could change the thermal decomposition process of DNTF while the positive E-field facilitates the breakdown of the C-NO₂ in DNTFⅣ molecules. Our work provides new insights into the relationship between the E-field and the intermolecular vibration energy transfer and decomposition mechanism of the DNTF system.