Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals

Theoretical Spectroscopic Study of Normal Raman and Charge Transfer Surface-Enhanced Raman Scattering (SERS) Spectra of the Adsorbed l- and d-Cysteine on the Chiral Au34 and Ag4@Au30 Nanoclusters: Chirality Discrimination

In this work, the discrimination of the enantiomers of cysteine (l- and d-CYS) using the chiral Au34 and Ag4@Au30 clusters was theoretically investigated in the gas phase and water. Two modes were considered for the interaction of each enantiomer with the clusters (via only its S atom or its S atom and NH2 group, simultaneously). The interaction energy (Eint) and adsorption energy (Ead) for the complexation of each enantiomer with the clusters for each interaction mode were calculated. Considering the calculated interaction energies, the interaction of d-CYS with Au34 is stronger than that of l-CYS with the same cluster. Also, it was observed that the substitution of the Au4 core of the Au34 cluster with the Ag4 cluster caused the increase of the interaction energy of l-CYS with the Ag4@Au30 cluster compared to the Au34 cluster, while the reverse trend was observed for d-CYS. Quantum theory of atoms in molecules (QTAIM) analysis was employed to calculate the interaction paths and their related bond critical points (BCPs) between the CYS enantiomers and the clusters to explain the difference between the interaction energy of the enantiomers with the clusters. The IR, normal Raman (NR), and surface-enhanced Raman scattering (SERS) spectra of the enantiomers interacting with the Au34 and Ag4@Au30 clusters were calculated, and the discrimination between l-CYS and d-CYS using the calculated spectra was explained. It was found that the discrimination of the enantiomers based on their interaction with the clusters is controlled by the charge transfer between the enantiomers and the clusters.

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.

Advances and Prospects in Understanding London Dispersion Interactions in Molecular Chemistry

London dispersion (LD) interactions are the main contribution of the attractive part of the van der Waals potential. Even though LD effects are the driving force for molecular aggregation and recognition, the role of these omnipresent interactions in structure and reactivity had been largely underappreciated over decades. However, in the recent years considerable efforts have been made to thoroughly study LD interactions and their potential as a chemical design element for structures and catalysis. This was made possible through a fruitful interplay of theory and experiment. This review highlights recent results and advances in utilizing LD interactions as a structural motif to understand and utilize intra- and intermolecularly LD-stabilized systems. Additionally, we focus on the quantification of LD interactions and their fundamental role in chemical reactions.

Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes

Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent cations to catalytic sites. However, modeling divalent cations in MM simulations has been challenging. The inclusion of explicit polarization was considered promising, but despite improvements over nonpolarizable force fields and despite the inclusion of "Nonbonded-fix (NB-fix)" corrections, errors in interaction energies of divalent cations with proteins remain large. Importantly, the application of these models fails to reproduce the experimental structural data on Mg2+·Protein·ATP complexes. Focusing on these complexes, here we provide a systematic assessment of the polarizable AMOEBA model and recommend critical changes that substantially improve its predictive performance. Our key results are as follows. We first show that our recent revision of the AMOEBA protein model (AMOEBABIO18-HFC), which contains high field corrections (HFCs) to induced dipoles, dramatically improves Mg2+-protein interaction energies, reducing the mean absolute error (MAE) from 17 to 10 kcal/mol. This further supports the general applicability of AMOEBABIO18-HFC. The inclusion of many-body NB-fix corrections further reduces MAE to 6 kcal/mol, which amounts to less than 2% error. The errors are estimated with respect to vdW-inclusive density functional theory that we benchmark against CCSD(T) calculations and experiments. We also present a new model of ATP with revised polarization parameters to better capture its high field response, as well as new vdW and dihedral parameters. The ATP model accurately predicts experimental Mg2+-ATP binding free energy in the aqueous phase and provides new insights into how Mg2+ associates with ATP. Finally, we show that molecular dynamics (MD) simulations of Mg2+·Kinase·ATP complexes carried out with these improvements lead to a better agreement in global and local catalytic site structures between MD and X-ray crystallography.

Unlocking the Potential of Nanoribbon-Based Sb2S3/Sb2Se3 van-der-Waals Heterostructure for Solar-Energy-Conversion and Optoelectronics Applications

High-performance nanosized optoelectronic devices based on van der Waals (vdW) heterostructures have significant potential for use in a variety of applications. However, the investigation of nanoribbon-based vdW heterostructures are still mostly unexplored. In this study, based on first-principles calculations, we demonstrate that a Sb2S3/Sb2Se3 vdW heterostructure, which is formed by isostructural nanoribbons of stibnite (Sb2S3) and antimonselite (Sb2Se3), possesses a direct band gap with a typical type-II band alignment, which is suitable for optoelectronics and solar energy conversion. Optical absorption spectra show broad profiles in the visible and UV ranges for all of the studied configurations, indicating their suitability for photodevices. Additionally, in 1D nanoribbons, we see sharp peaks corresponding to strongly bound excitons in a fashion similar to that of other quasi-1D systems. The Sb2S3/Sb2Se3 heterostructure is predicted to exhibit a remarkable power conversion efficiency (PCE) of 28.2%, positioning it competitively alongside other extensively studied two-dimensional (2D) heterostructures.

Single-Layer GaInSe3: Promising Water-Splitting Photocatalyst with Solar Conversion Efficiency over 30% from Theoretical Calculations

Hydrogen energy from solar water-splitting is known as an ideal method with which to address the energy crisis and global environmental pollution. Herein, the first-principles calculations are carried out to study the photocatalytic water-splitting performance of single-layer GaInSe3 under biaxial strains from -2% to +2%. Calculations reveal that single-layer GaInSe3 under various biaxial strains has electronic bandgaps ranging from 1.11 to 1.28 eV under biaxial strain from -2% to +2%, as well as a completely separated valence band maximum and conduction band minimum. Meanwhile, the appropriate band edges for water-splitting and visible optical absorption up to ~3 × 105 cm-1 are obtained under biaxial strains from -2% to 0%. More impressively, the solar conversion efficiency of single-layer GaInSe3 under biaxial strains from -2% to 0% reaches over 30%. The OER of unstrained single-layer GaInSe3 can proceed without co-catalysts. These demonstrate that single-layer GaInSe3 is a viable material for solar water-splitting.

ZnGeSe2 monolayer: water-splitting photocatalyst with ultrahigh solar conversion efficiency

Hydrogen production through solar water-splitting offers a clean and renewable solution to tackle the ongoing issues of energy scarcity and environmental pollution. Here, the solar water-splitting performance of the ZnGeSe2 monolayer was explored via first-principles calculations. Our calculated results reveal that the ZnGeSe2 monolayer embodies stable configurations and semiconducting properties with direct bandgaps ranging from 1.23 to 1.60 eV under the biaxial strain from -1% to +2%. The generated holes and electrons of the ZnGeSe2 monolayer are separately distributed because of the intrinsic dipole. The calculated band edges of the ZnGeSe2 monolayer are demonstrated to be favorable for solar water-splitting. Additionally, the ZnGeSe2 monolayer exhibits strong optical absorption in the whole visible region. The hydrogen and oxygen evolution reactions can be accomplished without cocatalysts. Of particular significance, the solar to hydrogen (STH) efficiency of the ZnGeSe2 monolayer reaches up to 32%, far exceeding the economic value (10%). In light of these hallmarks, the ZnGeSe2 monolayer is demonstrated as an excellent water-splitting photocatalyst.

How great is the stabilization of crowded polyphenylbiphenyls by London dispersion?

Decaphenylbiphenyl (1) and 2,2',4,4',6,6'-hexaphenylbiphenyl (2) are bulky molecules expected to be greatly destabilized by steric crowding. Herein, through a combined experimental and computational approach, we evaluate the molecular energetics of crowded biphenyls. This is complemented by the study of phase equilibria for 1 and 2. Compound 1 shows a rich phase behavior, displaying an unusual interconversion between two polymorphs. Surprisingly, the polymorph with distorted molecules of C₁ symmetry is found to have the highest melting point and to be the one that is preferentially formed. The thermodynamic results also indicate that the polymorph displaying the more regular D₂ molecular geometry has larger heat capacity and is probably the more stable at lower temperatures. The melting and sublimation data clearly reveal the weakening of cohesive forces in crowded biphenyls due to the lower molecular surface area. The experimental quantification of the intramolecular interactions in 1 and 2 indicated, using homodesmotic reactions, a molecular stabilization of about 30 kJ mol^-1. We attribute the origin of this stabilization in both compounds to the existence of two parallel-displaced π⋯π interactions between the ortho-phenyl substituents on each side of the central biphenyl. Computational calculations with dispersion-corrected DFT methods underestimate the stabilization in 1, unless the steric crowding is well balanced in a homodesmotic scheme. This work demonstrates that London dispersion forces are important in crowded aromatic systems, making these molecules considerably more stable than previously thought.

High thermoelectric performance of two-dimensional SiPGaS/As heterostructures

Thermoelectric technology holds great promise as a green and sustainable energy solution, generating electric power directly from waste heat. Herein, we investigate the thermoelectric properties of SiPGaS/As van der Waals heterostructures by using computations based on density functional theory and semiclassical Boltzmann transport theory. Our results show that both models of SiPGaS/As van der Waals heterostructures have low lattice thermal conductivity at room temperature (300 K). Applying 4% tensile strain to the models leads to a significant enhancement in the figure of merit (ZT), with model-I and model-II exhibiting ZT improvements of up to 24.5% and 14.8%, respectively. Notably, model-II outperforms all previously reported heterostructures in terms of ZT value. Additionally, we find that the maximum thermoelectric conversion efficiency (η) for model-II at 4% tensile strain reaches 23.98% at 700 K. Our predicted ZT_avg > 1 suggests that these materials have practical potential for thermoelectric applications over a wide temperature range. Overall, our findings offer valuable insights for designing better thermoelectric materials.

A Buckycatcher in Solution-A Computational Perspective

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

Ultralow diffusion barrier induced by intercalation in layered N-based cathode materials for sodium-ion batteries

Sodium-ion batteries (SIBs) have attracted huge attention due to not only the similar electrochemical properties to Lithium-ion batteries (LIBs) but also the abundant natural reserves of sodium. However, the high diffusion barrier has hindered its application. In this work, we have theoretically studied the relationship between the strain and the diffusion barrier/path of sodium ions in layered CrN₂ by first-principles calculation. Our results show that the strain can not only effectively decrease the diffusion barrier but also change the sodium diffusion path, which can be realized by alkali metal intercalation. Moreover, the diffusion barrier is as low as 0.04 eV with the Cs atoms embedding in layered CrN₂ (Cs_1/16CrN₂), suggesting an excellent candidate cathode for SIBs. In addition, the decrease of the barrier mainly originated from the fact that interlayer electronic coupling weakened with the increase of interlayer spacing. Our findings provide an effective way to enhance sodium diffusion performance, which is beneficial for the design of SIB electrode materials.

Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions

The reliability of molecular mechanics simulations to predict effects of ion binding to proteins depends on their ability to simultaneously describe ion-protein, ion-water, and protein-water interactions. Force fields (FFs) to describe protein-water and ion-water interactions have been constructed carefully and have also been refined routinely to improve accuracy. Descriptions for ion-protein interactions have also been refined, although in an a posteriori manner through the use of "nonbonded-fix (NB-fix)" approaches in which parameters from default Lennard-Jones mixing rules are replaced with those optimized against some reference data. However, even after NB-fix corrections, there remains a significant need for improvement. This is also true for polarizable FFs that include self-consistent inducible moments. Our recent studies on the polarizable AMOEBA FF suggested that the problem associated with modeling ion-protein interactions could be alleviated by recalibrating polarization models of cation-coordinating functional groups so that they respond better to the high electric fields present near ions. Here, we present such a recalibration of carbonyls, carboxylates, and hydroxyls in the AMOEBA protein FF and report that it does improve predictions substantially─mean absolute errors in Na⁺-protein and K⁺-protein interaction energies decrease from 8.7 to 5.3 and 9.6 to 6.3 kcal/mol, respectively. Errors are computed with respect to estimates from van der Waals-inclusive density functional theory benchmarked against high-level quantum mechanical calculations and experiments. While recalibration does improve ion-protein interaction energies, they still remain underestimated, suggesting that further improvements can be made in a systematic manner through modifications in classical formalism. Nevertheless, we show that by applying our many-body NB-fix correction to Lennard-Jones components, these errors are further reduced to 2.7 and 2.6 kcal/mol, respectively, for Na⁺ and K⁺ ions. Finally, we show that the recalibrated AMOEBA protein FF retains its intrinsic reliability in predicting protein structure and dynamics in the condensed phase.

Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7

New variants of SARS-CoV-2 are being reported worldwide. The World Health Organization has reported Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Omicron (B.1.1.529) as the variants of concern. There are speculations that the variants might evade the host immune responses induced by currently available vaccines and develop resistance to drugs under consideration. The first step of viral infection in COVID-19 occurs through the interaction of the spike protein's receptor-binding domain (RBD) with the peptidase domain of the human ACE-2 (hACE-2) receptor. This study aims to get a molecular-level understanding of the mechanism behind the increased infection rate in the alpha variant. We have computationally studied the spike protein interaction in both the wild-type and B.1.1.7 variant with the hACE-2 receptor using molecular dynamics and MM-GBSA based binding free energy calculations. The binding free energy difference shows that the mutant variant of the spike protein has increased binding affinity for the hACE-2 receptor (i.e. ΔG(N501Y,A570D) is in the range -7.2 to -7.6 kcal mol^-1) and the results were validated using Density functional theory. We demonstrate that with the use of state-of-the-art computational approaches, we can, in advance, predict the virulent nature of variants of SARS-CoV-2 and alert the world healthcare system.

Comparative study of Janus B2XY (X, Y = S, Se, Te) and F-BNBN-H monolayers for water splitting: revealing the positive and negative roles of the intrinsic dipole

It is widely recognized that the intrinsic dipole in two-dimensional (2D) photocatalysts promotes hydrogen production during water splitting. Herein, we wonder whether the intrinsic dipole plays a negative role in water splitting. In this work, we make a comparative study of the structural, electronic, and photocatalytic properties of Janus B₂XY (X, Y = S, Se, Te) and F-BNBN-H monolayers using first principles. Our theoretical results reveal that both B₂XY and F-BNBN-H monolayers exhibit spatially separated conduction band minimum (CBM) and valence band maximum (VBM), as well as vacuum level differences at the opposite surfaces due to the intrinsic dipole. The F-BNBN-H monolayer has excellent redox ability for water splitting, because its CBM is located at the surface with a lower vacuum level and its VBM is distributed on the opposite surface possessing a higher vacuum level. By sharp contrast, B₂XY monolayers have limited or vanishing redox ability, because their CBM is located at the surface with a higher vacuum level and their VBM is distributed on the opposite surface with a lower vacuum level. This work emphasizes the negative role of vacuum level differences of photocatalysts caused by the intrinsic dipole in water splitting.

Controllable Schottky barriers and contact types of BN intercalation layers in graphene/MoSi2As4 vdW heterostructures via applying an external electrical field

Graphene-based van der Waals (vdW) heterostructures have opened unprecedented opportunities for various device applications due to their rich functionalities and novel physical properties. Motivated by the successful synthesis of a MoSi₂N₄ monolayer (Science, 2020, 369, 670), in this work by means of first-principles calculations we construct and investigate the interfacial electronic properties of the graphene/MoSi₂As₄ vdW heterostructure, which is expected to be energetically favorable and stable. Our results show that the graphene/MoSi₂As₄ heterostructure forms an n-type Schottky contact with a low barrier of 0.12 eV, which is sensitive to the external electric field and the transformation from an n-type Schottky contact to a p-type one can be achieved at 0.2 V Å^-1. The small effective masses and strong optical absorption intensity indicate that the graphene/MoSi₂As₄ heterostructure will have a high carrier mobility and can be applied to high-speed FET. Importantly, we also show that the opening band gap can be achieved in the graphene/BN/MoSi₂As₄ heterostructure and the type-I band alignment can transform into type-II under an external electric field of -0.2 V Å^-1. These findings demonstrate that the graphene/MoSi₂As₄ heterostructure can be considered as a promising candidate for high-efficiency Schottky nanodevices.

Designing 3d metal oxides: selecting optimal density functionals for strongly correlated materials

Transition metal oxides (TMOs) have remarkable physicochemical properties, are non-toxic, and have low cost and high annual production, thus they are commonly studied for various technological applications. Density functional theory (DFT) can help to optimize TMO materials by providing insights into their electronic, optical and thermodynamic properties, and hence into their structure-performance relationships, over a wide range of solid-state structures and compositions. However, this is underpinned by the choice of the exchange-correlation (XC) functional, which is critical to accurately describe the highly localized and correlated 3d-electrons of the transition metals in TMOs. This tutorial review presents a benchmark study of density functionals (DFs), ranging from generalized gradient approximation (GGA) to range-separated hybrids (RSH), with the all-electron def2-TZVP basis set, comparing magneto-electro-optical properties of 3d TMOs against experimental observations. The performance of the DFs is assessed by analyzing the band structure, density of states, magnetic moment, structural static and dynamic parameters, optical properties, spin contamination and computational cost. The results disclose the strengths and weaknesses of the XC functionals, in terms of accuracy, and computational efficiency, suggesting the unprecedented PBE0-1/5 as the best candidate. The findings of this work contribute to necessary developments of XC functionals for periodic systems, and materials science modelling studies, particularly informing how to select the optimal XC functional to obtain the most trustworthy description of the ground-state electron structure of 3d TMOs.

How to Catch the Ball: Fullerene Binding to the Corannulene Pincer

The corannulene pincer (also known in the literature as the buckycatcher) is a fascinating system that may encapsulate, among other molecules, the C60 and C70 fullerenes. These complexes are held together by strong π-stacking interactions. Although these are quantum mechanical effects, their description by quantum chemical methods has proved very hard. We used three semi-empirical methods, PM6-D3H4X, PM6-D3H+ and GFN2-xTB, to model the interactions. Binding to fullerenes was extended to all open conformations of the buckycatcher, and with the proper choice of solvation model and partition functions, we obtained Gibbs free energies of binding that deviated by 1.0–1.5 kcal/mol from the experimental data. Adding three-body dispersion to PM6-D3H+ led to even better agreement. These results agree better with the experimental data than calculations using higher-level methods at a significantly lower fraction of the computational cost. Furthermore, the formation of adducts with C60 was studied using dynamical simulations, which helped to build a more complete picture of the behavior of the corannulene pincer with fullerenes. We also investigated the use of exchange-binding models to recover more information on this system in solution. Though the final Gibbs free energies in solution were worsened, gas-phase enthalpies and entropies better mirrored the experimental data.

A theoretical study on the proton affinity of sulfur ylides

The proton affinities of sulfoxide ylides, carbonyl ylides, allyl ylides, benzenyl ylides and heterocyclic ylides with typical substituents were investigated using the SOGGA11-X functional.

Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide

An anisotropic interlayer force field that describes the interlayer interactions in molybdenum disulfide (MoS2) is presented. The force field is benchmarked against density functional theory calculations for both bilayer and bulk systems within the Heyd-Scuseria-Ernzerhof hybrid density functional approximation, augmented by a nonlocal many-body dispersion treatment of long-range correlation. The parametrization yields good agreement with the reference calculations of binding energy curves and sliding potential energy surfaces for both bilayer and bulk configurations. Benchmark calculations for the phonon spectra of bulk MoS2 provide good agreement with experimental data, and the calculated bulk modulus falls in the lower part of experimentally measured values. This indicates the accuracy of the interlayer force field near equilibrium. Under external pressures up to 20 GPa, the developed force field provides a good description of compression curves. At higher pressures, deviations from experimental data grow, signifying the validity range of the developed force field.

High Anisotropic Optoelectronics in Two Dimensional Layered PbSnX2 (X = S/Se)

We systematically study the giant anisotropic optoelectronics in layered PbSnX₂ (X = S/Se). The highly anisotropic optoelectronics mainly originates from the asymmetric sublattices SnX, resulting in the anisotropy of photoelectronic properties with fascinating visible light absorption range in single-layer and bilayer PbSnX₂. We employ uniaxial strain in both the x and y directions and find an indirect-to-direct band gap transition, while the quasiparticle indirect band gap presents excellent linear scaling with biaxial strain in monolayer PbSnX₂. We also demonstrate ultrahigh anisotropic mobilities of electrons (μ_y > μ_x) and holes (μ_x > μ_y) in both single-layer and bilayer PbSnX₂ (X = S/Se), and spin-orbit coupling effects and the increase of layer number significantly reduce exciton binding energies and band gaps. Finally, the strong layer dependence of the band structure is clearly seen when the film thickness is less than 4 layers. Our results provide a fundamental understanding of highly anisotropic PbSnX₂ (X = S/Se) and show two potential candidates in photoelectric applications.

Regiochemical Effects on the Carbohydrate Binding and Selectivity of Flexible Synthetic Carbohydrate Receptors with Indole and Quinoline Heterocyclic Groups

Synthetic carbohydrate receptors (SCRs) that bind cell-surface carbohydrates could be used for disease detection, drug-delivery, and therapeutics, or for the site-selective modification of complex carbohydrates but their potential has not been realized because of remaining challenges associated with binding affinity and substrate selectivity. We have reported recently a series of flexible SCRs based upon a biaryl core with four pendant heterocyclic groups that bind glycans selectively through noncovalent interactions. Here we continue to explore the role of heterocycles on substrate selectivity by expanding our library to include a series of indole and quinoline heterocycles that vary in their regiochemistry of attachment to the biaryl core. The binding of these SCRs to a series of biologically-relevant carbohydrates was studied by 1H NMR titrations in CD2Cl2 and density-functional theory calculations. We find SCR030, SCR034 and SCR037 are selective, SCR031, SCR032, and SCR039 are strong binders, and SCR033, SCR035, SCR036, and SCR038 are promiscuous and bind weakly. Computational analysis reveals the importance of C-H⋯π and H-bonding interactions in defining the binding properties of these new receptors. By combining these data with those obtained from our previous studies on this class of flexible SCRs, we develop a series of design rules that account for the binding of all SCRs of this class and anticipate the binding of future, not-yet imagined tetrapodal SCRs.

Progress and challenges in ab initio simulations of quantum nuclei in weakly bonded systems

Atomistic simulations based on the first-principles of quantum mechanics are reaching unprecedented length scales. This progress is due to the growth in computational power allied with the development of new methodologies that allow the treatment of electrons and nuclei as quantum particles. In the realm of materials science, where the quest for desirable emergent properties relies increasingly on soft weakly bonded materials, such methods have become indispensable. In this Perspective, an overview of simulation methods that are applicable for large system sizes and that can capture the quantum nature of electrons and nuclei in the adiabatic approximation is given. In addition, the remaining challenges are discussed, especially regarding the inclusion of nuclear quantum effects (NQEs) beyond a harmonic or perturbative treatment, the impact of NQEs on electronic properties of weakly bonded systems, and how different first-principles potential energy surfaces can change the impact of NQEs on the atomic structure and dynamics of weakly bonded systems.

Efficient hierarchical models for reactivity of organic layers on semiconductor surfaces

Computational modeling of organic interface formation on semiconductors poses a challenge to a density functional theory-based description due to structural and chemical complexity. A hierarchical approach is presented, where parts of the interface are successively removed in order to increase computational efficiency while maintaining the necessary accuracy. First, a benchmark is performed to probe the validity of this approach for three model reactions and five dispersion corrected density functionals. Reaction energies are generally well reproduced by generalized gradient approximation-type functionals but accurate reaction barriers require the use of hybrid functionals. Best performance is found for the model system that does not explicitly consider the substrate but includes its templating effects. Finally, this efficient model is used to provide coverage dependent reaction energies and suggest synthetic principles for the prevention of unwanted growth termination reactions for organic layers on semiconductor surfaces.

First-principles calculations of hybrid inorganic-organic interfaces: from state-of-the-art to best practice

The computational characterization of inorganic-organic hybrid interfaces is arguably one of the technically most challenging applications of density functional theory. Due to the fundamentally different electronic properties of the inorganic and the organic components of a hybrid interface, the proper choice of the electronic structure method, of the algorithms to solve these methods, and of the parameters that enter these algorithms is highly non-trivial. In fact, computational choices that work well for one of the components often perform poorly for the other. As a consequence, default settings for one materials class are typically inadequate for the hybrid system, which makes calculations employing such settings inefficient and sometimes even prone to erroneous results. To address this issue, we discuss how to choose appropriate atomistic representations for the system under investigation, we highlight the role of the exchange-correlation functional and the van der Waals correction employed in the calculation and we provide tips and tricks how to efficiently converge the self-consistent field cycle and to obtain accurate geometries. We particularly focus on potentially unexpected pitfalls and the errors they incur. As a summary, we provide a list of best practice rules for interface simulations that should especially serve as a useful starting point for less experienced users and newcomers to the field.

Predictive QM/MM Modeling of Modulations in Protein-Protein Binding by Lysine Methylation

Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are sensitive to the extent of methylation. These sensitivities have been rationalized in terms of chemical and structural features present in the binding pockets of methyllysine binding domains. However, understanding their specific roles requires an energetic analysis. Here we propose a theoretical framework to combine quantum and molecular mechanics methods, and compute the effect of methylation on protein-protein binding free energies. The advantages of this approach are that it derives contributions from all local non-trivial effects of methylation on induction, polarizability and dispersion directly from self-consistent electron densities, and at the same time determines contributions from well-characterized hydration effects using a computationally efficient classical mean field method. Limitations of the approach are discussed, and we note that predicted free energies of fourteen out of the sixteen cases agree with experiment. Critical assessment of these cases leads to the following overarching principles that drive methylation-state recognition by protein domains. Methylation typically reduces the pairwise interaction between proteins. This biases binding toward lower methylated states. Simultaneously, however, methylation also makes it easier to partially dehydrate proteins and place them in protein-protein complexes. This latter effect biases binding in favor of higher methylated states. The overall effect of methylation on protein-protein binding depends ultimately on the balance between these two effects, which is observed to be tuned via several combinations of local features.

Theoretical study on adiabatic electron affinity of fatty acids

The AEA of saturated fatty acids, monounsaturated fatty acids, and polyunsaturated fatty acids with typical substituents were calculated by the ωB97X method.

Black Phosphorus as Multifaceted Advanced Material Nanoplatforms for Potential Biomedical Applications

Black phosphorus is one of the emerging members of two-dimensional (2D) materials which has recently entered the biomedical field. Its anisotropic properties and infrared bandgap have enabled researchers to discover its applicability in several fields including optoelectronics, 3D printing, bioimaging, and others. Characterization techniques such as Raman spectroscopy have revealed the structural information of Black phosphorus (BP) along with its fundamental properties, such as the behavior of its photons and electrons. The present review provides an overview of synthetic approaches and properties of BP, in addition to a detailed discussion about various types of surface modifications available for overcoming the stability-related drawbacks and for imparting targeting ability to synthesized nanoplatforms. The review further gives an overview of multiple characterization techniques such as spectroscopic, thermal, optical, and electron microscopic techniques for providing an insight into its fundamental properties. These characterization techniques are not only important for the analysis of the synthesized BP but also play a vital role in assessing the doping as well as the structural integrity of BP-based nanocomposites. The potential role of BP and BP-based nanocomposites for biomedical applications specifically, in the fields of drug delivery, 3D printing, and wound dressing, have been discussed in detail to provide an insight into the multifunctional role of BP-based nanoplatforms for the management of various diseases, including cancer therapy. The review further sheds light on the role of BP-based 2D platforms such as BP nanosheets along with BP-based 0D platforms-i.e., BP quantum dots in the field of therapy and bioimaging of cancer using techniques such as photoacoustic imaging and fluorescence imaging. Although the review inculcates the multimodal therapeutic as well as imaging role of BP, there is still research going on in this field which will help in the development of BP-based theranostic platforms not only for cancer therapy, but various other diseases.

Density Functional Theory for Molecule-Metal Surface Reactions: When Does the Generalized Gradient Approximation Get It Right, and What to Do If It Does Not

While density functional theory (DFT) is perhaps the most used electronic structure theory in chemistry, many of its practical aspects remain poorly understood. For instance, DFT at the generalized gradient approximation (GGA) tends to fail miserably at describing gas-phase reaction barriers, while it performs surprisingly well for many molecule-metal surface reactions. GGA-DFT also fails for many systems in the latter category, and up to now it has not been clear when one may expect it to work. We show that GGA-DFT tends to work if the difference between the work function of the metal and the molecule's electron affinity is greater than ∼7 eV and to fail if this difference is smaller, with sticking of O₂ on Al(111) being a spectacular example. Using dynamics calculations we show that, for this system, the DFT problem may be solved as done for gas-phase reactions, i.e., by resorting to hybrid functionals, but using screening at long-range to obtain a correct description of the metal. Our results suggest the GGA error in the O₂ + Al(111) barrier height to be functional driven. Our results also suggest the possibility to compute potential energy surfaces for the difficult-to-treat systems with computationally cheap nonself-consistent calculations in which a hybrid functional is applied to a GGA density.

Computational Investigations of Dispersion Interactions between Small Molecules and Graphene-like Flakes

We investigate dispersion interactions in a selection of atomic, molecular, and molecule-surface systems, comparing high-level correlated methods with empirically corrected density functional theory (DFT). We assess the efficacy of functionals commonly used for surface-based calculations, with and without the D3 correction of Grimme. We find that the inclusion of the correction is essential to get meaningful results, but there is otherwise little to distinguish between the functionals. We also present coupled-cluster quality interaction curves for H₂, NO₂, H₂O, and Ar interacting with large carbon flakes, acting as models for graphene surfaces, using novel absolutely localized molecular orbital based methods. These calculations demonstrate that the problems with empirically corrected DFT when investigating dispersion appear to compound as the system size increases, with important implications for future computational studies of molecule-surface interactions.

Improved description of ligand polarization enhances transferability of ion-ligand interactions

The reliability of molecular mechanics (MM) simulations in describing biomolecular ion-driven processes depends on their ability to accurately model interactions of ions simultaneously with water and other biochemical groups. In these models, ion descriptors are calibrated against reference data on ion-water interactions, and it is then assumed that these descriptors will also satisfactorily describe interactions of ions with other biochemical ligands. The comparison against the experiment and high-level quantum mechanical data show that this transferability assumption can break down severely. One approach to improve transferability is to assign cross terms or separate sets of non-bonded descriptors for every distinct pair of ion type and its coordinating ligand. Here, we propose an alternative solution that targets an error-source directly and corrects misrepresented physics. In standard model development, ligand descriptors are never calibrated or benchmarked in the high electric fields present near ions. We demonstrate for a representative MM model that when the polarization descriptors of its ligands are improved to respond to both low and high fields, ligand interactions with ions also improve, and transferability errors reduce substantially. In our case, the overall transferability error reduces from 3.3 kcal/mol to 1.8 kcal/mol. These improvements are observed without compromising on the accuracy of low-field interactions of ligands in gas and condensed phases. Reference data for calibration and performance evaluation are taken from the experiment and also obtained systematically from "gold-standard" CCSD(T) in the complete basis set limit, followed by benchmarked vdW-inclusive density functional theory.

KAgX (X = S, Se): High-Performance Layered Thermoelectric Materials for Medium-Temperature Applications

Monolayer KAgX are a class of novel two-dimensional (2D) layered materials with efficient optical absorption and superior carrier mobility, signifying their potential application prospect in photovoltaic (PV) and thermoelectric (TE) fields. Motivated by the recent theoretical studies on the KAgX monolayer, we carried out systematic investigations on the TE performance of KAgS and KAgSe monolayers, employing density functional theory (DFT) and semiclassical Boltzmann transport equation (BTE). For both KAgSe and KAgS monolayers, large Grüneisen parameters, low group velocities, and short phonon scattering time greatly hinder their heat transport and result in an ultralow thermal conductivity, 0.26 and 0.33 W m^-1 K^-1 at 300 K, respectively. A twofold degeneracy appearing at the Γ point and the abrupt slope of the density of states (DOS) near the Fermi level give rise to high Seebeck coefficients of KAgX monolayers. Due to the ultralow thermal conductivity and excellent electronic transport performance, the ZT values as high as 4.65 (3.11) and 4.05 (2.63) at 500 (300) K in the n-type doping for KAgSe and KAgS monolayers are obtained. The exceptional performance of KAgX monolayers sheds light on their immense potential applications in the medium-temperature (around 300-500 K) thermoelectric devices and greatly stimulates further experimental synthesis and validation.

Ab Initio Evaluation of Complexation Energies for Cyclodextrin-Drug Inclusion Complexes

We investigated the reliability of ab initio methods to predict the binding energies of molecular encapsulation complexes. Vast possibilities for the docking conformations were screened down to a couple of geometries using a semiempirical docking simulation. For the candidates, we applied density functional theory (DFT) with several exchange-correlation (XC) functionals to evaluate the binding energy. We carefully selected and compared the functionals to elucidate the role of the characteristic factors in achieving the XC effects. It is clarified that the improper combination in XC with D3 dispersion force correction leads to overbinding. For achieving a proper combination, the exchange interaction over the longer range to avoid the overbinding was found to be important.

Static- and frequency-dependent NLO properties of dithienothiophene and thienothiophene bridges — A computational investigation

We have explored detailed linear and nonlinear optical properties of push-pull systems bearing thienothiophene and dithienothiophene spacers. By using density functional theory (DFT), frequency-dependent strategies were applied to examine the polarizability ([Formula: see text] and hyperpolarizability ([Formula: see text] and [Formula: see text]. The set of global and range-separated hybrid functionals with different Hartree–Fock (HF) exchange percentage at two basis sets cc-pVDZ and cc-pVTZ were used to evaluate the nonlinear optical (NLO) properties. The observed trends in the absorption maxima supported by perturbation potential analysis; as the absorption maxima increases, the respective amplitude potential decreases. For the investigated compounds, [Formula: see text]-conjugation along with the type of substituted acceptor plays a crucial role in the enhancement of NLO properties. The presence of acceptor group and length of conjugation increase between the D and A group; the first- and second-order intrinsic hyperpolarizability increases, leads to enhanced first- as well as second-order hyperpolarizability. Bond length alternation (BLA)/bond order alteration (BOA) exploration suggested that compounds attain cyanine limit. The trends in NLO properties for investigated compounds are supported by chemical reactivity descriptors, hardness and hyperhardness analysis. The polarizability is linearly correlated with the hyperpolarizability parameters ([Formula: see text] and [Formula: see text] and shows a good regression coefficient by figures of merit analysis.

Structural and electronic properties of CuII, CoII, and NiII-containing chelate-based ionic liquids

Potential applications of chelate-based ionic liquids depend on the structural and electronic properties of this class of liquid materials. Due to the large size of chelated metal anions, the high number of potential interaction sites could lead to complex intermolecular interactions, but metal-based anions have many degrees of freedom, and they have great potential in the structural modification of the physical properties of ionic liquids. To explore the influence of varying the metal center of anions and the length of carbon chains of cationic species, four single crystal structures of chelate-based ionic liquids, ([C₁₀mim][M(F₆-acac)₃], M = Cu, Co, and Ni) and [C₆mim][Cu(F₆-acac)₃] were obtained. Taking these as the initial configurations, theoretical efforts were made to understand the structural and electronic properties. The hydrogen bonding energies of the primary hydrogen bonding interaction, in the range of 17.7-20.9 kJ mol^-1, follow the order of [C₁₀mim][Ni(F₆-acac)₃] < [C₁₀mim][Co(F₆-acac)₃] <[C₁₀mim][Cu(F₆-acac)₃], and [C_nmim][Cu(F₆-acac)₃] (n≠ 10) < [C₁₀mim][Cu(F₆-acac)₃], while the experimental viscosities exhibit an opposite trend. Furthermore, by NBO analysis, the more negative charge on the oxygen atoms of anions shows the stronger hydrogen bonding of imidazolium with C²H. The reliability of the theoretical method was supported by the comparison between the simulated and experimental infrared and UV/vis spectra. This work is useful in increasing the understanding of the structure-property relationship of chelate-based ionic liquids and furthering the rational design of novel ionic liquids.

Surface Adsorption and Vacancy in Tuning the Properties of Tellurene

The emerging two-dimensional tellurene has been demonstrated to be a promising candidate for photoelectronic devices. However, there is a lack of comprehensive insight into the effects of vacancies and common adsorbates (i.e., O₂ and H₂O) in ambient conditions, which play a crucial role in semiconducting devices. In this work, with the aid of first-principles calculations, we demonstrate that H₂O and O₂ molecules behave qualitatively differently on tellurene, while water adsorption can be remarkably promoted by adjacent preadsorbed O₂. Upon the formation of Te vacancies, the adsorption of both O₂ and H₂O molecules is enhanced. More importantly, the existence of H₂O and Te vacancies can dramatically facilitate the dissociation of O₂, suggesting that tellurene may be readily oxidized in humid conditions. In addition, it is found that the electronic properties of tellurene are well preserved upon either H₂O or O₂ adsorption on the surface. In sharp contrast, vacancies enable significant modification on the band structure. Specifically, an indirect-to-direct band gap transition is found at a vacancy concentration of 5.3%.

From the perspectives of DFT calculations, thermodynamic modeling, and kinetic Monte Carlo simulations: the interaction between hydrogen and Sc2C monolayers

In this study, we have examined the adsorption properties of hydrogen on pristine Sc₂C monolayers by DFT calculations. Based on these calculations, we have proposed a thermodynamic model to estimate the hydrogen storage capability within the typical ranges for the operating temperature and pressure. Our thermodynamic modeling has shown that the maximum uptake of usable hydrogen could reach up to 7.2 wt% under cryogenic conditions. When calculating the usable hydrogen uptake, we have taken into consideration that, under realistic operating conditions, not all hydrogen adsorbed on pristine Sc₂C can be desorbed from the surface, as some surface-adsorbate interactions are too strong. On the other hand, the interaction between the usable hydrogen and Sc₂C appears to be too weak to reach the targets for the year 2025 set by the US Department of Energy (5.5 wt% at operating temperatures between 233 K and 358 K and delivery pressures of up to 12 bar). According to the modeling results, one needs to decrease the temperature to 120 K to reach 5.5 wt% hydrogen uptake at 12 bar. The results obtained with the thermodynamic model have been confirmed with a kinetic Monte Carlo simulation, which has also been used to estimate the time scale of the hydrogen adsorption and desorption processes. In addition, we have also evaluated the changes in the electronic structure of the Sc₂C monolayer upon adsorbing hydrogen. As the band gap of Sc₂C changes significantly upon adsorbing H₂, Sc₂C may have more potential as a hydrogen detector instead of as a hydrogen storage material.

Establishing the accuracy of density functional approaches for the description of noncovalent interactions in biomolecules

Biomolecules have complex structures, and noncovalent interactions are crucial to determine their conformations and functionalities.

Ultralow lattice thermal conductivity and high thermoelectric performance of monolayer KCuTe: a first principles study

Monolayer KCuTe is a new-type of two-dimensional (2D) semiconductor material with high carrier mobility and large power energy conversion efficiencies, suggesting its potential application in thermoelectric (TE) and photoelectric fields. Based on the density functional theory (DFT) and semiclassical Boltzmann transport equation, the electronic and phonon transport properties of monolayer KCuTe are systematically studied. Our results show that it possesses an ultralow lattice thermal conductivity value of nearly ∼0.13 W m⁻¹ K⁻¹ at 300 K, mainly attributed to its small phonon group velocity, large Grüneisen parameters, and strong phonon–phonon scattering. Furthermore, the intralayer opposite phonon vibrations greatly restrict the heat transport. Monolayer KCuTe shows an ideal direct band gap of ∼1.21 eV, and a high twofold degeneracy appearing at the Γ point gives a high Seebeck coefficient of ∼2070 μV K⁻¹, leading to high TE performance. Using the transport coefficients together with constant electron relaxation time, the figure of merit (ZT) can reach 2.71 at 700 K for the p-type doping, which is comparable to the well-known TE material SnSe (2.6 ± 0.3 at 935 K). Our theoretical studies may provide perspectives to TE applications of monolayer KCuTe and stimulate further experimental synthesis.

The excellent thermoelectric performance of monolayer KCuTe is discovered by first-principles study for the first time.