Density functional theory with London dispersion corrections

Theoretical and Experimental Study of Different Side Chains on 3,4-Ethylenedioxythiophene and Diketopyrrolopyrrole-Derived Polymers: Towards Organic Transistors

In this research, two polymers of P1 and P2 based on monomers consisting of thiophene, 3,4-Ethylenedioxythiophene (EDOT) and diketopyrrolopyrrole (DPP) are designed and obtained via Stille coupling polycondensation. The material shows excellent coplanarity and structural regularity due to the fine planarity of DPP itself and the weak non-covalent bonding interactions existing between the three units. Two different lengths of non-conjugated side chains are introduced and this has an effect on the intermolecular chain stacking, causing the film absorption to display different characteristic properties. On the other hand, the difference in the side chains does not have a significant effect on the thermal stability and the energy levels of the frontier orbitals of the materials, which is related to the fact that the materials both feature extremely high conjugation lengths and specific molecular compositions. Microscopic investigations targeting the side chains provide a contribution to the further design of organic semiconductor materials that meet device requirements. Tests based on organic transistors show a slight difference in conductivity between the two polymers, with P2 having better hole mobility than P1. This study highlights the importance of the impact of side chains on device performance, especially in the field of organic electronics.

Boosting Energy-Transfer Processes via Dispersion Interactions

The generation of open-shell intermediates under mild conditions has opened broad synthetic opportunities during this century. However, these reactive species often require a case specific and tailored tuning of experimental parameters in order to efficiently convert substrates into products. We report a general approach that can overcome these ubiquitous limitations for several visible-light promoted energy-transfer processes. The use of either naphthalene (5-20 equiv.) or simple binaphthyl derivatives (10-30 mol %) greatly increases their efficiency, giving rise to a new strategy for catalysis. The trend is consistent among different media, photocatalysts, light sources and substrates, allowing one to improve existing methods, to more easily optimize conditions for new ones, and, moreover, to disclose otherwise inaccessible reaction pathways.

Massively parallel implementation of gradients within the random phase approximation: Application to the polymorphs of benzene

The Random-Phase approximation (RPA) provides an appealing framework for semi-local density functional theory. In its Resolution-of-the-Identity (RI) approach, it is a very accurate and more cost-effective method than most other wavefunction-based correlation methods. For widespread applications, efficient implementations of nuclear gradients for structure optimizations and data sampling of machine learning approaches are required. We report a well scaling implementation of RI-RPA nuclear gradients on massively parallel computers. The approach is applied to two polymorphs of the benzene crystal obtaining very good cohesive and relative energies. Different correction and extrapolation schemes are investigated for further improvement of the results and estimations of error bars.

Pressure-Induced Aggregation of Associating Liquids as a Driving Force Enhancing Hydrogen Bond Cooperativity

The behavior of hydrogen bonds under extreme pressure is still not well understood. Until now, the shift of the stretching vibration band of the X-H group (X = the donor atom) in infrared spectra has been attributed to the variation in the length of the covalent X-H bond. Herein, we combined infrared spectroscopy and X-ray diffraction experimental studies of two H-bonded liquid hexane derivatives, i.e., 2-ethyl-1-hexanol and 2-ethyl-1-hexylamine, in diamond anvil cells at pressures up to the GPa level, with molecular dynamics simulations covering similar thermodynamic conditions. Our findings revealed that the observed changes in the X-H stretching vibration bands under compression are not primarily due to H-bond shortening resulting from increased density but mainly due to cooperative enhancement of H-bonds caused by intensified molecular clustering. This sheds new light on the nature of H-bond interactions and the structure of liquid molecular systems under compression.

Balance between Physical Interpretability and Energetic Predictability in Widely Used Dispersion-Corrected Density Functionals

We assess the performance of different dispersion models for several popular density functionals across a diverse set of noncovalent systems, ranging from the benzene dimer to molecular crystals. By analyzing the interaction energies and their individual components, we demonstrate that there exists variability across different systems for empirical dispersion models, which are calibrated for reproducing the interaction energies of specific systems. Thus, parameter fitting may undermine the underlying physics, as dispersion models rely on error compensation among the different components of the interaction energy. Energy decomposition analyses reveal that, the accuracy of revPBE-D3 for some aqueous systems originates from significant compensation between dispersion and charge transfer energies. However, revPBE-D3 is less accurate in describing systems where error compensation is incomplete, such as the benzene dimer. Such cases highlight the propensity for unpredictable behavior in various dispersion-corrected density functionals across a wide range of molecular systems, akin to the behavior of force fields. On the other hand, we find that SCAN-rVV10, a targeted-dispersion approach, affords significant reductions in errors associated with the lattice energies of molecular crystals, while it has limited accuracy in reproducing structural properties. Given the ubiquitous nature of noncovalent interactions and the key role of density functional theory in computational sciences, the future development of dispersion models should prioritize the faithful description of the dispersion energy, a shift that promises greater accuracy in capturing the underlying physics across diverse molecular and extended systems.

Incorporation of Diketopyrrolopyrrole into Polythiophene for the Preparation of Organic Polymer Transistors

Polythiophene, as a class of potential electron donor units, is widely used in organic electronics such as transistors. In this work, a novel polymeric material, PDPPTT-FT, was prepared by incorporating the electron acceptor unit into the polythiophene system. The incorporation of the DPP molecule assists in improving the solubility of the material and provides a convenient method for the preparation of field effect transistors via subsequent solution processing. The introduction of fluorine atoms forms a good intramolecular conformational lock, and theoretical calculations show that the structure displays excellent co-planarity and regularity. Grazing incidence wide-angle X-ray (GIWAXS) results indicate that the PDPPTT-FT is highly crystalline, which facilitates carrier migration within and between polymer chains. The hole mobility of this π-conjugated material is as high as 0.30 cm2 V-1 s-1 in organic transistor measurements, demonstrating the great potential of this polymer material in the field of optoelectronics.

The Unimolecular Chemistry of Methyl Chloroformate Ions and Neutrals: A Story of Near-Threshold Decomposition

The near-threshold dissociation of ionized and neutral methyl chloroformate (CH3COOCl, MCF) was explored with imaging photoelectron photoion coincidence spectroscopy. The threshold photoelectron spectrum (TPES) for MCF was acquired for the first time; the large geometry changes upon ionization of MCF result in a broad, poorly defined TPES. Franck-Condon simulations are consistent with an adiabatic ionization energy (IE) of 10.90 ± 0.05 eV. Ionized MCF dissociates by chlorine atom loss at a measured 0 K appearance energy (AE) of 11.30 ± 0.01 eV. Together with the above IE, this AE suggests a reaction barrier of 0.40 ± 0.05 eV, consistent with the SVECV-f12 computational result of 0.41 eV. At higher internal energies, the loss of CH3O• becomes competitive due to its lower entropy of activation. Pyrolysis of neutral MCF formed the anticipated major products CH3Cl + CO2 (R1) and the minor products HCl + CO + CH2O (R2). The thermal decomposition products were identified by their photoion mass-selected threshold photoelectron spectrum (ms-TPES). Possible reaction pathways were explored computationally to confirm the dominant ones: R1 proceeds by a concerted Cl atom migration via a four-membered transition state in agreement with the mechanism proposed in the literature. R2 is a two-step reaction first yielding 2-oxiranone by HCl loss, which then decomposes to CH2O and CO. Kinetic modeling of the neutral decomposition could simulate the observed reactions only if the vibrational temperature of the MCF was assumed not to cool in the expansion.

Light-Driven Enantioselective Carbene-Catalyzed Radical-Radical Coupling

An enantioselective carbene-catalyzed radical-radical coupling of acyl imidazoles and racemic Hantzsch esters is disclosed. This method involves the coupling of an N-heterocyclic carbene-derived ketyl radical and a secondary sp3 -carbon radical and allows access to chiral α-aryl aliphatic ketones in moderate-to-good yields and enantioselectivities without any competitive epimerization. The utility of this protocol is highlighted by the late-stage functionalization of various pharmaceutical compounds and is further demonstrated by the transformation of the enantioenriched products to biologically relevant molecules. Computational investigations reveal the N-heterocyclic carbene controls the double-facial selectivity of the ketyl radical and the alkyl radicals, respectively.

Low-loss contacts on textured substrates for inverted perovskite solar cells

Inverted perovskite solar cells (PSCs) promise enhanced operating stability compared to their normal-structure counterparts1-3. To improve efficiency further, it is crucial to combine effective light management with low interfacial losses4,5. Here we develop a conformal self-assembled monolayer (SAM) as the hole-selective contact on light-managing textured substrates. Molecular dynamics simulations indicate that cluster formation during phosphonic acid adsorption leads to incomplete SAM coverage. We devise a co-adsorbent strategy that disassembles high-order clusters, thus homogenizing the distribution of phosphonic acid molecules, and thereby minimizing interfacial recombination and improving electronic structures. We report a laboratory-measured power conversion efficiency (PCE) of 25.3% and a certified quasi-steady-state PCE of 24.8% for inverted PSCs, with a photocurrent approaching 95% of the Shockley-Queisser maximum. An encapsulated device having a PCE of 24.6% at room temperature retains 95% of its peak performance when stressed at 65 °C and 50% relative humidity following more than 1,000 h of maximum power point tracking under 1 sun illumination. This represents one of the most stable PSCs subjected to accelerated ageing: achieved with a PCE surpassing 24%. The engineering of phosphonic acid adsorption on textured substrates offers a promising avenue for efficient and stable PSCs. It is also anticipated to benefit other optoelectronic devices that require light management.

ConfSolv: Prediction of Solute Conformer-Free Energies across a Range of Solvents

Predicting Gibbs free energy of solution is key to understanding the solvent effects on thermodynamics and reaction rates for kinetic modeling. Accurately computing solution free energies requires the enumeration and evaluation of relevant solute conformers in solution. However, even after generation of relevant conformers, determining their free energy of solution requires an expensive workflow consisting of several ab initio computational chemistry calculations. To help address this challenge, we generate a large data set of solution free energies for nearly 44,000 solutes with almost 9 million conformers calculated in 41 different solvents using density functional theory and COSMO-RS and quantify the impact of solute conformers on the solution free energy. We then train a message passing neural network to predict the relative solution free energies of a set of solute conformers, enabling the identification of a small subset of thermodynamically relevant conformers. The model offers substantial computational time savings with predictions usually substantially within 1 kcal/mol of the free energy of the solution calculated by using computational chemical methods.

Interactions between Metals and Eudistomins of Ascidian Origin: A Computational Study

Ascidians are marine animals that adopt unusual techniques to deter predation. The three main methods are sequestration of unusual metals, high concentrations of sulfuric acid/sulfate ions in tunicate cells, and the presence of eudistomins. In this study, we hypothesize that ascidians sequester metals in their sulfate form, and the complexation of eudistomins with the metals could liberate the sulfate ion. Three representative metal aqua ions were chosen, viz., vanadyl, uranyl, and thorium ions, as well as four simple eudistomins which act as bidentate ligands, viz., eudistomin-W, debromoeudistomin-K, eudistomidin-C, and eudistomidin-B. By designing 7 model reactions, we tested our hypothesis using density functional theory (DFT) methods PBE-D3, BLYP, and B3LYP. The ΔG values of the model reactions provide strong support for our hypothesis. To verify the hypothesis further, we calculated the metal-eudistomin interactions with Be, Zn, and Pb. Based on our results, we suggest that ascidians may not prefer any particular metal. In addition, despite using different DFT functionals, we have observed similar ΔG values for each case. With our work, we have successfully used computational tools in our attempt to understand the unique behavior of ascidians.

Local Oxidation States in {FeNO}6-8 Porphyrins: Insights from DMRG/CASSCF-CASPT2 Calculations

A first DMRG/CASSCF-CASPT2 study of a series of paradigmatic {FeNO}6, {FeNO}7, and {FeNO}8 heme-nitrosyl complexes has led to substantial new insight as well as uncovered key shortcomings of the DFT approach. By virtue of its balanced treatment of static and dynamic correlation, the calculations have provided some of the most authoritative information available to date on the energetics of low- versus high-spin states of different classes of heme-nitrosyl complexes. Thus, the calculations indicate low doublet-quartet gaps of 1-4 kcal/mol for {FeNO}7 complexes and high singlet-triplet gaps of ≳20 kcal/mol for both {FeNO}6 and {FeNO}8 complexes. In contrast, DFT calculations yield widely divergent spin state gaps as a function of the exchange-correlation functional. DMRG-CASSCF calculations also help calibrate DFT spin densities for {FeNO}7 complexes, pointing to those obtained from classic pure functionals as the most accurate. The general picture appears to be that nearly all the spin density of Fe[P](NO) is localized on the Fe, while the axial ligand imidazole (ImH) in Fe[P](NO)(ImH) pushes a part of the spin density onto the NO moiety. An analysis of the DMRG-CASSCF wave function in terms of localized orbitals and of the resulting configuration state functions in terms of resonance forms with varying NO(π*) occupancies has allowed us to address the longstanding question of local oxidation states in heme-nitrosyl complexes. The analysis indicates NO(neutral) resonance forms [i.e., Fe(II)-NO0 and Fe(III)-NO0] as the major contributors to both {FeNO}6 and {FeNO}7 complexes. This finding is at variance with the common formulation of {FeNO}6 hemes as Fe(II)-NO+ species but is consonant with an Fe L-edge XAS analysis by Solomon and co-workers. For the {FeNO}8 complex {Fe[P](NO)}-, our analysis suggests a resonance hybrid description: Fe(I)-NO0 ↔ Fe(II)-NO-, in agreement with earlier DFT studies. Vibrational analyses of the compounds studied indicate an imperfect but fair correlation between the NO stretching frequency and NO(π*) occupancy, highlighting the usefulness of vibrational data as a preliminary indicator of the NO oxidation state.

An all-metal fullerene: [K@Au12Sb20]5

The C60 fullerene molecule has attracted tremendous interest for its distinctive nearly spherical structure. By contrast, all-metal counterparts have been elusive: Fullerene-like clusters composed of noncarbon elements typically suffer from instability, resulting in more compact geometries that require multiple embedded atoms or external ligands for stabilization. In this work, we present the synthesis of an all-metal fullerene cluster, [K@Au12Sb20]5-, using a wet-chemistry method. The cluster's structure was determined by single crystal x-ray diffraction, which revealed a fullerene framework consisting of 20 antimony atoms. Theoretical calculations further indicate that this distinct cluster exhibits aromatic behavior.

Consistent density functional theory-based description of ion hydration through density-corrected many-body representations

Delocalization error constrains the accuracy of density functional theory in describing molecular interactions in ion-water systems. Using Na+ and Cl- in water as model systems, we calculate the effects of delocalization error in the SCAN functional for describing ion-water and water-water interactions in hydrated ions, and demonstrate that density-corrected SCAN (DC-SCAN) predicts n-body and interaction energies with an accuracy approaching coupled cluster theory. The performance of DC-SCAN is size-consistent, maintaining an accurate description of molecular interactions well beyond the first solvation shell. Molecular dynamics simulations at ambient conditions with many-body MB-SCAN(DC) potentials, derived from the many-body expansion, predict the solvation structure of Na+ and Cl- in quantitative agreement with reference data, while simultaneously reproducing the structure of liquid water. Beyond rationalizing the accuracy of density-corrected models of ion hydration, our findings suggest that our unified density-corrected MB formalism holds great promise for efficient DFT-based simulations of condensed-phase systems with chemical accuracy.

Accurate Quantum Chemical Reaction Energies for Lithium-Mediated Electrolyte Decomposition and Evaluation of Density Functional Approximations

An important concern related to the performance of Li-ion batteries is the formation of a solid electrolyte interphase on the surface of the anode. This film is formed from the decomposition of electrolytes and can have important effects on the stability and performance. Here, we evaluate the decomposition pathway of ethylene carbonate and related organic electrolyte molecules using a series of density functional approximations and correlated wave function (WF) methods, including the coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and auxiliary-field quantum Monte Carlo (AFQMC). We find that the transition state barrier associated with ring opening varies widely across different functionals, ranging from 3.01 to 17.15 kcal/mol, which can be compared to the value of 12.84 kcal/mol predicted by CCSD(T). This large variation underscores the importance of benchmarking against accurate WF methods. A performance comparison of all of the density functionals used in this study reveals that the M06-2X-D3 (a meta-hybrid GGA), CAM-B3LYP-D3 (a range-separated hybrid), and B2GP-PLYP-D3 (a double hybrid) perform the best, with average errors of about 1.50-1.60 kcal/mol compared to CCSD(T). We also compared the performance of the WF methods that are more scalable than CCSD(T), finding that DLPNO-CCSD(T) and phaseless AFQMC with a DFT trial wave function exhibit average errors of 1.38 and 1.74 kcal/mol, respectively.

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.