Density Functional Theory Level Research Articles

Nuclear quantum effects on zeolite proton hopping kinetics explored with machine learning potentials and path integral molecular dynamics

Proton hopping is a key reactive process within zeolite catalysis. However, the accurate determination of its kinetics poses major challenges both for theoreticians and experimentalists. Nuclear quantum effects (NQEs) are known to influence the structure and dynamics of protons, but their rigorous inclusion through the path integral molecular dynamics (PIMD) formalism was so far beyond reach for zeolite catalyzed processes due to the excessive computational cost of evaluating all forces and energies at the Density Functional Theory (DFT) level. Herein, we overcome this limitation by training first a reactive machine learning potential (MLP) that can reproduce with high fidelity the DFT potential energy surface of proton hopping around the first Al coordination sphere in the H-CHA zeolite. The MLP offers an immense computational speedup, enabling us to derive accurate reaction kinetics beyond standard transition state theory for the proton hopping reaction. Overall, more than 0.6 μs of simulation time was needed, which is far beyond reach of any standard DFT approach. NQEs are found to significantly impact the proton hopping kinetics up to ~473 K. Moreover, PIMD simulations with deuterium can be performed without any additional training to compute kinetic isotope effects over a broad range of temperatures.

Effects of the protonation and the polar solvation on the molecular properties of methyl orange: A density functional theory study

AbstractMethyl orange (MO) and its protonated derivatives were investigated at the density functional theory (DFT) level using CAM‐B3LYP functional and 6‐311 + G(d,p) basis sets; their absorption spectra in aqueous solution were simulated, their relative stabilities in both the gas phase and the polar solutions were calculated, and the activation energy barrier for the cis‐to‐trans isomerization in both phases were computed. Except the protonation at the amino group, all the protonated isomers show a bathochromic shift of the most intense absorption peak. In the gas phase, the sulfonate unit turns out to be the most favorable proton acceptor. In the polar solutions, however, azo groups are more effective to accept the proton. The protonation at the azo N atom next to the phenyl‐sulfonate group significantly reduces the energy barrier for the cis‐to‐trans conversion in the aqueous solution, which suggests a swift conversion in the ground state.

A comprehensive discussion on photophysical properties of dihydropyridines: Experimental and theoretical studies

In this article, the photophysical properties of DHPs, including 1,2-DHPs and 1,4-DHPs, were studied experimentally and theoretically. Their structural differences bring about different photophysical properties, and also lead to different photochemical properties. Specifically, a series of different substituted 1,2-DHPs and 1,4-DHPs were synthesized to measure their UV–Vis absorption and fluorescence emission spectra in diluted solutions and theoretical calculations were performed at the density functional theory (DFT) level. To describe the reactivities of the DHPs, time-dependent density functional theory (TDDFT) was used to optimize their ground- and excited-state structures, and their electronic excitation energies were calculated at the B3LYP-D3/def2-TZVP level. Frontier molecular orbitals and electron-hole distribution analyses were used to illustrate the electron transition types. The differences between the ground- and excited-state structures of the different DHPs were characterized by carrying out a root-mean-square-deviation (RMSD) analysis.

Dicarbon defect in hexagonal boron nitride monolayer—a theoretical study

A comprehensive theoretical study of the lowest electronic vertical excitations of the CBCN defect in the monolayer of hexagonal boron nitride has been performed. Both the periodic boundary conditions approach and the finite-cluster simulation of the defect have been utilized at the density-functional theory (DFT) level. Clusters of increasing sizes have been used in order to estimate artefacts resulting from edge effects. The stability of the results with respect to several density functionals and various basis sets has been also examined. High-level ab initio calculations with methods like equation-of-motion coupled cluster method with single and double excitations (EOM-CCSD), algebraic-diagrammatic construction to the second order (ADC(2)), and time-dependent approximate coupled cluster theory to the second order (TD-CC2) were performed for the smallest clusters. It turns out that TD-DFT with the CAM-B3LYP functional gives similar lowest excitation energies as EOM-CCSD, ADC(2), and TD-CC2. The lowest excitation energies resulting from the periodic-boundary calculation utilizing the Bethe–Salpeter equation are in agreement with the results for finite clusters. The analysis of important configurations and transition densities shows that for all studied methods, the lowest excited state is localized on two carbon atoms and their closest neighbours and has a large dipole transition moment. The optimized geometries for the lowest two excited states indicate that in both cases, the carbon–carbon bond becomes a single bond, while for the second excited state, additionally one from boron–nitrogen bonds loses its partially double character. The calculation of the excitation energies at the respective optimal geometry reveals that these two energies become about 0.5 eV lower than vertical excitations from the ground-state geometry.

Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsenate Salt of 4-Aminopyridine

In this work, a structural and electronic properties of a novel organic arsenate template by 4-aminopyridine, with the general formula (C5H7N2)(C5H8N2)[AsO4]·H2O ((4-APH)(4-APH2)[AsO4]·H2O) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The examination of the vibrational spectrum was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. Besides, the thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO–LUMO energy gap, NLO characteristic and Hirshfeld surface analysis were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Molecular docking studies were also conducted as part of this study. The theoretical results showed an excellent agreement with the experimental values.

Ab Initio Study of Adsorption of Polymers on Metal–Organic Framework Surfaces

We present a computational study of metal–organic framework (MOF)/polymer interfaces in order to better understand the phenomena relevant to optimizing the design of MOF/polymer mixed-matrix membrane (MMM) materials. In this pursuit, we study adsorption of models of polymers Kapton and 6FDA-Durene to models of MOF surfaces both with and without coordinatively unsaturated metal sites existing on the surface (ZIF-8 and Co-BDC, respectively) at the density functional theory (DFT) level. To do this, we develop and tune models of polymers that are DFT-accessible, establishing a method for creating models of polymers that is transferable beyond these systems for use in studying MMMs, identifying some limits to this method. Through this work, we find that while polymer interactions with MOF surfaces may be expected to be dispersion-dominated, in the presence of coordinatively unsaturated metals on the surface, electronic and electrostatic effects may play a significant role, consistent with the previous literature in this area. We additionally find that while polymer model terminations often do not strongly affect the qualitative behavior at the MOF/polymer interface, an accurate electronic representation of the polymers may be critical for the development of force field-based tools to model MMMs and for a detailed understanding of the interactions in some cases.

Structural variety of Cu (II), Ni (II), and Co (II) complexes of a hydrazone based on 5‐acetyl‐4‐hydroxy‐2H‐1,3‐thiazine‐2,6(3H)‐dione: Synthesis, spectroscopic, density functional theory, antitumor, and docking studies

New nickel (II), cobalt (II), and several copper (II) complexes have been synthesized from the hydrazone ligand (AHTDSH; H2L); which obtained from 5‐acetyl‐4‐hydroxy‐2H‐1,3‐thiazine‐2,6(3H)‐dione with salicylaldehyde hydrazone. The structures of H2L ligand and the prepared complexes were confirmed by spectroscopic and analytical techniques. The ligand behaves as bis (monobasic bidentate) and dibasic tetradentate chelating agent via azomethine nitrogen and phenolic oxygen atoms. Octahedral geometries have been assigned for the prepared complexes. The Coats–Redfern equations were used to estimate the kinetic parameters (Ea, A, H, S, and G) of the thermal decomposition stages. The molecular structural characteristics of the ligand and its metal complexes were estimated based on density functional theory (DFT) level implemented in the Gaussian 09 software at B3LYP/6‐311G(d,p) level and the theoretical data were connected with the results of the experimental work. The anticancer activity of AHTDSH ligand and its complexes was demonstrated toward HepG2 cell lines. The interaction between the chemical and the active site of the CDK2 kinase was examined using a docking study of the hydrazone ligand and its complexes.

First-principles theory of electrochemical capacitance

The differential capacitance comprises the most relevant thermodynamic information about an electrochemical system. Classical approaches to describe electrochemical capacitance have difficulties to combine the treatment of the ionic contribution of the electrolyte with the electronic contribution of the electrode. Moreover, different approaches are typically required for the description of the double-layer capacitance, on the one hand, and the pseudocapacitive contribution due to adsorption or intercalation of reactive species, on the other. In the present work, a new approach to describe electrochemical capacitance from first principles is developed. The treatment of a general electrochemical system at the level of multicomponent density-functional theory (MCDFT) yields an exact analytical expression for the total capacitance of the system, which corresponds to a formal series-circuit partitioning into “quantum” capacitance contributions of the density of states of electrons and ions, the (mean-field) electrostatic capacitance, as well as capacitance contributions of exchange and correlation among all active species. It is shown that the classical expression of the double-layer capacitance involving the interfacial Galvani potential is obtained in the limit of extended electrode and electrolyte regions. Importantly, the present formalism also describes systems with confined electrode and electrolyte phases, where the definition of the (classical) inner potentials of the electrode and electrolyte domains becomes problematic. Moreover, the new approach unifies the treatment of double-layer capacitance and pseudocapacitance resulting from reactive processes.

Electronic State Spectroscopy of Nitromethane and Nitroethane.

High-resolution photoabsorption cross-sections in the 3.7-10.8 eV energy range are reinvestigated for nitromethane (CH3NO2), while for nitroethane (C2H5NO2), they are reported for the first time. New absorption features are observed for both molecules which have been assigned to vibronic excitations of valence, Rydberg, and mixed valence-Rydberg characters. In comparison with nitromethane, nitroethane shows mainly broad absorption bands with diffuse structures, which can be interpreted as a result of the side-chain effect contributing to an increased number of internal degrees of freedom. New theoretical quantum chemical calculations performed at the time-dependent density functional theory (TD-DFT) level were used to qualitatively help interpret the recorded photoabsorption spectra. From the photoabsorption cross-sections, photolysis lifetimes in the terrestrial atmosphere have been obtained for both compounds. Relevant internal conversion from Rydberg to valence character is noted for both molecules, while the nuclear dynamics of CH3NO2 and C2H5NO2 along the C-N reaction coordinate have been evaluated through potential energy curves at the TD-DFT level of theory, showing that the pre-dissociative character is more prevalent in nitromethane than in nitroethane.

Size and Quality of Quantum Mechanical Data Set for Training Neural Network Force Fields for Liquid Water.

Molecular dynamics simulations have been used in different scientific fields to investigate a broad range of physical systems. However, the accuracy of calculation is based on the model considered to describe the atomic interactions. In particular, ab initio molecular dynamics (AIMD) has the accuracy of density functional theory (DFT) and thus is limited to small systems and a relatively short simulation time. In this scenario, Neural Network Force Fields (NNFFs) have an important role, since they provide a way to circumvent these caveats. In this work, we investigate NNFFs designed at the level of DFT to describe liquid water, focusing on the size and quality of the training data set considered. We show that structural properties are less dependent on the size of the training data set compared to dynamical ones (such as the diffusion coefficient), and a good sampling (selecting data reference for the training process) can lead to a small sample with good precision.

Predicting the structures and vibrational spectra of molecular crystals containing large molecules with the generalized energy-based fragmentation approach.

The generalized energy-based fragmentation (GEBF) approach under periodic boundary conditions (PBCs) has been developed to facilitate calculations of molecular crystals containing large molecules. The PBC-GEBF approach can help predict structures and properties of molecular crystals at different theory levels by performing molecular quantum chemistry calculations on a series of non-periodic subsystems constructed from the studied systems. A more rigorous formula of the forces on translational vectors of molecular crystals was proposed and implemented, enabling more reliable predictions of crystal structures. Our benchmark results on several typical molecular crystals show that the PBC-GEBF approach could reproduce the forces on atoms and the translational vectors and the optimized crystal structures from the corresponding conventional periodic methods. The improved PBC-GEBF approach is then applied to predict the crystal structures and vibrational spectra of two molecular crystals containing large molecules. The PBC-GEBF approach can provide a satisfactory description on the crystal structure of a molecular crystal containing 312 atoms in a unit cell at density-fitting second-order Møller-Plesset perturbation theory and density functional theory (DFT) levels and the infrared vibrational spectra of another molecular crystal containing 864 atoms in a unit cell at the DFT level. The PBC-GEBF approach is expected to be a promising theoretical tool for electronic structure calculations on molecular crystals containing large molecules.

Unraveling the Intrinsic Biocidal Activity of the SiO2-Ag Composite against SARS-CoV-2: A Joint Experimental and Theoretical Study.

The COVID-19 pandemic has emerged as an unprecedented global healthcare emergency, demanding the urgent development of effective materials to inactivate the SARS-CoV-2 virus. This research was planned to disclose the remarkable biocidal activity of SiO2-Ag composites incorporated into low-density polyethylene. For this purpose, a joint experimental and theoretical [based on first-principles calculations at the density functional theory (DFT) level] study is performed. Biological assays showed that this material eliminatesStaphylococcus aureusand SARS-CoV-2 virus in just 2 min. Here, we investigate a previously unexplored process that we postulate may occur along the O2 and H2O adsorption and activation processes of pure and defective SiO2-Ag surfaces for the generation of reactive oxygen species (ROS). The obtained results help us to predict the nature of ROS: superoxide anion radicals, •O2-, hydroxyl radicals, •OH, and hydroperoxyl radicals, •HO2, that destroy and degrade the structure of the SARS-COV-2 virus. This is consistent with the DFT studies, where the energetic, electronic, and magnetic properties of the intermediates show a feasible formation of ROS. Present findings are expected to provide new insights into the relationship among the structure, property, and biocidal activity of semiconductor/metal SiO2-Ag composites.

Computational investigation on the antioxidant activities and on the Mpro SARS-CoV-2 non-covalent inhibition of isorhamnetin.

In the present work, we report a computational study on some important chemical properties of the flavonoid isorhamnetin, used in traditional medicine in many countries. In the course of the study we determined the acid-base equilibria in aqueous solution, the possible reaction pathways with the •OOH radical and the corresponding kinetic constants, the complexing capacity of copper ions, and the reduction of these complexes by reducing agents such as superoxide and ascorbic anion by using density functional level of theory Density Functional Theory. Finally, the non-covalent inhibition ability of the SARS-CoV-2 main protease enzyme by isorhamnetin was examined by molecular dynamics (MD) and docking investigation.

Phase stability of Fe from first principles: Atomistic spin dynamics coupled with ab initio molecular dynamics simulations and thermodynamic integration

The calculation of free energies from first principles in materials is a formidable task which enables the prediction of phase stability with high accuracy; these calculations are complicated in magnetic materials by the interplay of electronic, magnetic, and vibrational degrees of freedom. In this work, we show the feasibility and accuracy of the calculation of phase stability in magnetic systems with ab initio methods and thermodynamic integration by sampling the magnetic and vibrational phase space with coupled atomistic spin dynamics-ab initio molecular dynamics (ASD-AIMD) simulations [Stockem et al., PRL 121, 125902 (2018)], where energies and interatomic forces are calculated with density functional theory (DFT). We employ the method to calculate the phase stability of Fe at ambient pressure from 800 K up to 1800 K. The Gibbs free energy difference between fcc and bcc Fe at zero pressure as a function of temperature is calculated carrying out thermodynamic integration over temperature on the energies at the DFT level from ASD-AIMD, using a reference free energy difference calculated in the paramagnetic state at temperatures much higher than the magnetic transition temperatures with thermodynamic integration over stress-strain variables with disordered local moment (DLM)-AIMD simulations. We show the importance of the magnetic ordering temperature of bcc Fe on the $\alpha$ to $\gamma$ structural transition temperature, whereas the $\gamma$ to $\delta$ transition is well reproduced independently of the exchange interactions. The Gibbs free energy difference between the two structures is within 5 meV/atom from the CALPHAD estimate, and both transition temperatures are reproduced within 150 K. The present work paves the way to free energy calculations in magnetic materials from first principles with accuracy in the order of 1 meV/atom.

Influence of the Nature of the Lipid Building Blocks on the Second-Order Nonlinear Optical Responses of an Embedded Di-8-ANEPPS Probe.

The extensive collection of lipids found in cell membranes is justified by the fact that each lipid contributes to their overall structure, dynamics, and properties and so to the biological processes taking place within them. It also showcases that, in order to deepen our understanding of membranes, we need to have a tool to differentiate lipid bilayers of varying composition. In this work, we investigate a suite of single-component saturated glycerophospholipids varying only in their headgroup structure by analyzing the second harmonic generation (SHG) nonlinear optical (NLO) response of a probe, di-8-ANEPPS, embedded into the membranes. The seven hydrophilic heads chosen (phosphatidylcholine (PC), phosphatidylethanolamine (PE), diaglycerol (GL), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), and phosphatidyc acid (PA)) represent all the major headgroups that are part of mammalian plasma membranes and provide an assortment of neutral, zwiterrionic, and charged species. First, molecular dynamics simulations revealed that the lipidic arrangement is strongly sensitive to the nature of the hydrophilic head and less to the variety in the hydrophobic region. Membranes exhibiting drastically opposite structural properties can be pointed out: 1,2-dihexadecanoyl-rac-glycerol (DPGL) is the thickest and most ordered and aligned system, whereas 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) (DPPG) is thinnest and least ordered and aligned system. The structural analyses are then confronted with the molecular NLO responses, β, computed at the time-dependent density functional theory (TDDFT) level. As the orientation of the chromophore is impacted by the various degrees of order within the lipid bilayers, the diagonal component of the β tensor parallel to the bilayer normal, βZZZ, is as well. In the end, this computational approach provides insights into the link between lipid building blocks and the NLO responses of the embedded dye.

The entropic penalty for associative reactions and their physical treatment during routine computations.

A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 ΔrG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol-1 (classic) and underestimated by 2 kcal mol-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol-1 lower than barriers obtained with WFT.

Relationship between the Electric Polarizability and Aromaticity of Metallocene-Containing Macrocycles

Magnetically induced ring currents, aromaticity, as well as polarizability and second hyperpolarizability of the metallocenothiaporphyrins with transition metals of group VIII (Fe, Ru) and isoelectronic cations of group IX (Со+, Rh+) and metallocene-containing annulenes ((C5H5)2М[n = 18–24], where M is Fe, Co+) have been studied computationally at Density Functional level of Theory (DFT). The calculations show that the value of average polarizability of the studied compounds depends on their character of the aromaticity. Aromatic structures are characterized by larger polarizability than their corresponding antiaromatic congeners. The average polarizability of metallocenothiaporphyrins also depends on the magnitude of magnetically induced ring currents, which quantify the degree of electron delocalization. An increase in the number of 𝜋-electrons in conjugation pathway plays a key role in the growth of polarizability. Aromaticity also influences on the second hyperpolarizability of metallocene-containing annulenes. In the case of compounds with the same number of conjugated electrons, the second hyperpolarizability is larger for more aromatic systems. To conclude, our results pinpoint the importance of electron delocalization on the polarizability and second hyperpolarizability of the studied metallocene-containig macrocycles

The structure of DNA fragments: Quantum-chemical modelling

In this review, we analyze and systematize our computational studies of the nucleic acid duplex formations and thermodynamic stability under the different factors of investigation. The proposed structural models of mini-helix contains N nucleobase pairs (N = 3-5); QM structural data suggest that the helical conformations of mini-helix adopt geometrical parameters comparable to those of natural A- and B-DNA forms under specific conditions as micro hydration and charge compensation. The gas-phase models adopt non regular conformations between the helical form and a ladder form.. The natural helical shape of DNA mini-helix is stabilized by the presence of counterions or by explicit micro-hydration of the major and minor groves. The presence of aqueous solution is shown as a minor factor for the helical shape formation. The studies are performed at the level of density functional theory.

Computational study on the mechanisms of inhibition of SARS-CoV-2 Mpro by aldehyde warheads based on DFT.

SARS-CoV-2 main protease, Mpro, plays a crucial role in the virus replication cycle, making it an important target for antiviral research. In this study, a simplified model obtained through truncation is used to explore the reaction mechanism of aldehyde warhead compounds inhibiting Mpro at the level of density functional theory. According to the calculation results, proton transfer (P_T)-nucleophilic attack (N_A) is the rate-determining step in the entire reaction pathway. The water molecule that plays a catalytic role occupies the oxyanion hole, which is unfavorable for the aldehyde warhead to approach the Cys145 SH. Through a hypothetical study of substituting the main chain NH with methylene, it is further confirmed that the P_T-N_A is a proton transfer-dominated process accompanied by a nucleophilic attack reaction. In this process, the oxyanion hole serves only to stabilize the aldehyde oxygen anion and therefore does not have a significant impact on the activation free energy barrier of the step. Our research results provide a unique perspective for understanding the covalent inhibition reaction of the Mpro active site. This study also offers theoretical guidance for the design of new Mpro covalent inhibitors.

Insights into the ruthenium-catalysed selective reduction of cardanol derivatives via transfer hydrogenation: a density functional theory study

The detailed mechanism for ruthenium-catalysed selective reduction of cardanol derivatives by transfer hydrogenation has been fully characterised at the B3PW91-D3/ECP2/PCM//B3PW91/ECP1 level of density functional theory.