The assessment and application of an approach to noncovalent interactions: the energy decomposition analysis (EDA) in combination with DFT of revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set

Study on the Effect of Cations on the Surface Energy of Nano-SiO2 Particles for Oil/Gas Exploration and Development Based on the Density Functional Theory

Although nano SiO2 exhibits excellent application potential in the field of oil and gas exploration and development, such as drilling fluid, enhanced oil/gas recovery, etc., it is prone to agglomeration and loses its effectiveness due to the action of cations in saline environments of oil and gas reservoirs. Therefore, it is crucial to study the mechanism of the change in energy between nano SiO2 and cations for its industrial application. In this paper, the effect of cations (Na+, K+, Ca2+, and Mg2+) on the surface energy of nano SiO2 particles is investigated from the perspective of molecular motion and electronic change by density functional theory. The results are as follows: Due to the electrostatic interactions, cations can migrate towards the surface of nano SiO2 particles. During the migration process, monovalent cations are almost unaffected by water molecules, and they can be directly adsorbed on the surface by nano SiO2 particles. However, when divalent cations migrate from a distance to the surface of nano SiO2 particles, they can combine with water molecules to create an energy barrier, which can prevent them from moving forward. When divalent cations break through the energy barrier, the electronic kinetic energy between them and nano SiO2 particles changes more strongly, and the electrons carried by them are more likely to break through the edge of the atomic nucleus and undergo charge exchange with nano SiO2 particles. The change in interaction energy is more intense, which can further disrupt the configuration stability of nano SiO2. The interaction energy between cations and nano SiO2 particles mainly comes from electrostatic energy, followed by Van der Waals energy. From the degree of influence of four cations on nano SiO2 particles, the order from small to large is as follows: K+ < Na+ < Mg2+ < Ca2+. The research results can provide a theoretical understanding of the interaction between nano SiO2 particles and cations during the application of nano SiO2 in the field of oil and gas exploration and development.

Long but Strong C-C Single Bonds: Challenges for Theory

Theoretical challenges in describing molecules with anomalously long single C-C bonds are analyzed in terms of the relative contributions of stabilizing and destabilizing intramolecular interactions. Diamondoid dimers that are stable despite the presence of C-C bonds up to 1.7 Å long, as well as other bulky molecules stabilized due to intramolecular noncovalent interactions (London dispersions) are discussed. The unexpected stability of highly crowded molecules, such as diamondoid dimers and tert-butyl-substituted hexaphenylethanes, calls for reconsideration of the "steric effect" traditionally thought to destabilize the molecule. Alternatively, "steric attraction" helps to understand bonding in sterically overloaded molecules, whose structural and energetic analysis requires a proper theoretical description of noncovalent interactions.

Uncovering the mechanism of selective stabilization of high-energy diastereoisomers via inclusion

Supramolecular systems may be used to stabilize otherwise unstable isomers to find alternative synthetic pathways. It has been reported that cucurbit[8]uril can stabilize trans-I and trans-II CuII cyclam, whereas trans-III is the only non-substituted trans CuII cyclam diastereoisomer found outside of the host molecule experimentally. Quantum chemistry methods can provide valuable insight into the intermolecular interactions involved in these inclusion complexes. All five possible trans diastereoisomers of CuII cyclam were studied within the host molecule to calculate the interaction energy and free energy of association for each complex. The relative free energies of the five free cyclams confirm that trans-I and trans-II are the most energetically accessible diastereoisomers from the initial trans-III starting point. Energy decomposition analysis was used to identify the attractive and repulsive interactions between cyclam and cucurbit[8]uril and showed that trans-II encounters repulsive forces almost three times greater than trans-I, which may explain the 7:3 ratio of trans-I to trans-II within cucurbit[8]uril that occurs experimentally. Optimized complex geometries with trans-III, IV, and V show that the cyclams protrude out of cucurbit[8]uril, whereas trans-I and trans-II become more encapsulated and elongate the host, suggesting that the position of the cyclam is extremely important when forming non-covalent interactions. Our results agree with the experimental findings and provide greater insight into why the most stable isolated cyclam diastereoisomer, trans-III, does not form a complex.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00214-023-03077-7.

Insight into the Formation of Cocrystal and Salt of Tenoxicam from the Isomer and Conformation

Tenoxicam (TNX) is a new non-steroidal anti-inflammatory drug that shows a superior anti-inflammatory effect and has the advantages of a long half-life period, a fast onset of action, a small dose, complete metabolism, and good tolerance. Some compounds often have tautomerism, and different tautomers exist in different crystalline forms. TNX is such a compound and has three tautomers. TNX always exists as the zwitterionic form in cocrystals. When the salt is formed, TNX exists in the enol form, which exhibits two conformations depending on whether a proton is gained or lost. Currently, the crystal structure of the keto form is not in the Cambridge Structural Database (CSD). Based on the analysis of existing crystal structures, we derived a simple rule for what form of TNX exists according to the pKa value of the cocrystal coformer (CCF) and carried out validation tests using three CCFs with different pKa values, including p-aminosalicylic acid (PAS), 3,5-dinitrobenzoic acid (DNB), and 2,6-dihydroxybenzoic acid (DHB). The molecular surface electrostatic potential (MEPS) was combined with the pKa rule to predict the interaction sites. Finally, two new cocrystals (TNX-PAS and TNX-DNB) and one salt (TNX-DHB) of TNX were obtained as expected. The differences between the cocrystals and salt were distinguished by X-ray diffraction, vibration spectra, thermal analysis, and dissolution measurements. To further understand the intermolecular interactions in these cocrystals and salt, the lattice energy and energy decomposition analysis (EDA) were used to explain them from the perspective of energy. The results suggest that the melting point of the CCF determines that of the cocrystal or salt, the solubility of the CCF itself plays an important role, and the improvement of the solubility after salt formation is not necessarily better than that of API or its cocrystals.

A novel organic carbon accumulation mechanism in croplands in the Yellow River Delta, China

The trends and mechanisms of organic carbon changes in coastal delta croplands are not yet clear due to the complexity physicochemical processes in soil. In this study, combing powder x-ray diffraction (XRD), microbial analysis, and density functional theory in quantum mechanics, we proposed a novel mechanism underlying OC accumulation. We investigated changes of three kinds of organic carbon (OC)-dissolved organic carbon (DOC), light fraction organic carbon (LFOC), and heavy fraction organic carbon (HFOC) in the Yellow River Delta croplands. We found that HFOC, dominant in coastal delta cropland soil, formed at different ages and its density increased with increasing reclamation time. Yet, DOC and LFOC had no significant increase or decrease tendency. Moreover, in coastal delta croplands, HFOC accumulation might be a complex progress, including the loss of indigenous OC and the accumulation of newly input OC. Based on these results, we proposed that although root exudative DOC (organic acids) could cause the indigenous OC loss by forming a specific microbial community, it still was a source of HFOC and promoted the OC accumulation. More importantly, based on density functional theory, we verified that these root exudative organic acids could adsorb on SiO₂ together with crystalline Fe oxides (Fe_c) to form aggregates. The finding could explain the phenomenon that the XRD results showed samples were compounds of SiO₂, Fe_c, and OC and the accumulation of HFOC in coastal delta croplands. By revealing a new OC accumulation mechanism in coastal delta croplands, this study provides novel insights into the mechanism of OC dynamics in coastal delta croplands and the global carbon budget.

Electrochemical sensing behavior of graphdiyne nanoflake towards uric acid: a quantum chemical approach

Though the gas sensing applications of graphdiyne have widely reported; however, the biosensing utility of graphdiyne needs to be explored. This study deals with the sensitivity of graphdiyne nanoflake (GDY) towards the uric acid (UA) within the density functional framework. The uric acid is allowed to interact with graphdiyne nanoflake from all the possible orientations. Based on these interacting geometries, the complexes are differentiated with naming, i.e., UA1@GDY, UA2@GDY, UA3@GDY, and UA4@GDY (Fig. 1). The essence of interface interactions of UA on GDY is derived by computing geometric, energetic, electronic, and optical properties. The adsorbing affinity of complexes is evaluated at ωB97XD/6-31 + G(d, p) level of theory. The stabilities of the complexes are quantified through the interaction energies (E_int) with reasonable accuracy. The calculated E_int of the UA1@GDY, UA2@GDY, UA3@GDY, and UA4@GDY complexes are - 31.13, - 25.87, - 20.59, and - 16.54 kcal/mol, respectively. In comparison with geometries, it is revealed that the higher stability of complexes is facilitated by π-π stacking. Other energetic analyses including symmetry adopted perturbation theory (SAPT), noncovalent interaction index (NCI), and quantum theory of atoms in molecule (QTAIM) provide the evidence of dominating dispersion energy in stabilizing the resultant complexes. The HOMO-LUMO energies, NBO charge transfer, and UV-vis analysis justify the higher electronic transition in UA1@GDY, plays a role of higher sensitivity of GDY towards the π-stacked geometries over all other possible interaction orientations. The present findings bestow the higher sensitivity of GDY towards uric acid via π-stacking interactions. Fig. 1 Optimized geometries (with interaction distances in Å) of UA@GDY complexes.

Kinetic and Potential Energy Contributions to a Chemical Bond from the Charge and Energy Decomposition Scheme of Extended Transition State Natural Orbitals for Chemical Valence

This work provides novel physical insight into the nature of a chemical bond by exploring qualitative and quantitative relations between the natural orbitals for chemical valence (NOCV)-based deformation density bonding channels Δρ _i ( i = σ, π, δ, etc.) and the corresponding kinetic Δ T_i and potential energy Δ V_i contributions within the charge and energy decomposition scheme ETS-NOCV implemented in the Kohn-Sham-based Amsterdam Density Functional (ADF) package. It is determined that interfragment dative and covalent-type electron charge reorganizations upon formation of a series of strong and weak bonds employing main-group elements are due to lowering of the negative kinetic energy contributions, as opposed to the intrafragment polarizations (e.g., hyperconjugations in ethane), which are, in contrary, driven by the potential energy (electrostatic) component. Complementary, formation of π-contributions in N₂ is accompanied by lowering of both kinetic and potential energy constituents. Remarkably, well-known globally stabilizing back-donation (M → ligand, where M is a transition metal) and donation (ligand → M) processes, ubiquitous in organometallic species, have been discovered for the first time to be driven by the opposite Δ T_i/Δ V_i mechanisms, namely, the former contribution is associated with the negative kinetic term (which outweighs the positive potential energy), whereas the latter charge delocalization into electrophilic transition metals leads to an attractive electrostatic stabilization (and positive kinetic energy).

Theory and practice of modeling van der Waals interactions in electronic-structure calculations

The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree-Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree-Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience.

Protonation state and fine structure of the active site determine the reactivity of dehydratase: hydration and isomerization of β-myrcene catalyzed by linalool dehydratase/isomerase from Castellaniella defragrans

Linalool dehydratase/isomerase (LinD) from Castellaniella defragrans is a bifunctional enzyme that catalyzes the hydration of β-myrcene to (S)-linalool and isomerization of (S)-linalool to geraniol.

Extended lead(ii) architectures engineered via tetrel bonding interactions

The cooperative action of multiple non-covalent interactions allowed for the assembly of a new series of Pb^II coordination compounds.

DFT study of CO2 and H2O co-adsorption on carbon models of coal surface

The moisture content of coal affects the adsorption capacity of CO₂ on the coal surface. Since the hydrogen bonds are formed between H₂O and oxygen functional group, the H₂O cluster more easily adsorbs on the coal micropore than CO₂ molecule. The coal micropores are occupied by H₂O molecules that cannot provide extra space for CO₂ adsorption, which may leads to the reduction of CO₂ adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO₂ and adsorbed H₂O molecule are not clear. Density functional theory (DFT) calculations were performed to elucidate the effect of adsorbed H₂O to CO₂ adsorption. This study reports some typical coal-H₂O···CO₂ complexes, along with a detailed analysis of the geometry, energy, electrostatic potential (ESP), atoms in molecules (AIM), reduced density gradient (RDG), and energy decomposition analysis (EDA). The results show that H₂O molecule can more stably adsorb on the aromatic ring surface than CO₂ molecule, and the absolute values of local ESP maximum and minimum of H₂O cluster are greater than CO₂. AIM analysis shows a detailed interaction path and strength between atoms in CO₂ and H₂O, and RDG analysis shows that the interactions among CO₂, H₂O, and coal model belong to weak van der Waals force. EDA indicates that electrostatic and long-range dispersion terms play a primary role in the co-adsorption of CO₂ and H₂O. According to the DFT calculated results without considering micropore structure and functional group, it is shown that the adsorbed H₂O can promote CO₂ adsorption on the coal surface. These results demonstrate that the micropore factor plays a dominant role in affecting CO₂ adsorption capacity, the attractive interaction of adsorbed H₂O to CO₂ makes little contribution.

DFT study of water adsorption on lignite molecule surface

High moisture content is a main characteristic of low-rank coal, such as lignite. Numerous oxygen containing functional groups in lignite make it represent some special properties, and these functional groups affect the adsorption mechanisms of water molecules on lignite surface. This study reports some typical water · · · lignite conformations, along with a detailed analysis of the geometry, electrostatic potential distribution, reduced density gradient of interaction, and interaction energy decomposition. The results show that water molecules tend to aggregate around functional groups, and hydrogen bonds play a dominant role in the interaction. The adsorption energy of water cluster on lignite surface is larger than that of isolated water molecule, a good linear relationship between the interaction distance and adsorption energy of layers has been found. Since water is a polar molecule, the local minima and maxima of electrostatic potential in conformations increase along with more water adsorbing on lignite surface. Reduced density gradient analysis shows that H-bonds, van der Waals interaction, and a little steric make up the interaction between water cluster and lignite molecule. In these studied conformations which mainly are H-bond complexes, electrostatic and exchange repulsion play a dominant role, whereas polarization and dispersion make relatively small contribution to the interaction. Attractive and repulsive interaction both affect the stability of water · · · lignite conformations.

Anion-driven tetrel bond-induced engineering of lead(ii) architectures with N′-(1-(2-pyridyl)ethylidene)nicotinohydrazide: experimental and theoretical findings

A new series of Pb^II coordination compounds was assembled with the N′-(1-(2-pyridyl)ethylidene)nicotinohydrazide ligand and various auxiliary inorganic counterions.

Photocurrent in Multilayered Assemblies of Porphyrin-Fullerene Covalent Dyads: Evidence for Channels for Charge Transport

Specially designed porphyrin-fullerene dyads have been synthesized to verify literature predictions based on quantum chemistry calculations that certain porphyrin-fullerene dyads are able to self-arrange into specific structures providing channels for charge transport in a bulk mass of organic compound. According to AFM and SEM data, the newly synthesized compounds were indeed prone to some kind of self-arrangement, although to a lesser degree than was expected. A dispersion corrected DFT study of the molecular non-covalent interactions performed at the DFT-D3 (B3LYP, 6-31G*) level of theory showed that the least energy corresponded to head-to-head dimers, with close contacts of porphyrin-porphyrin and fullerene-fullerene fragments, thus providing a unit building block of the channel for charge transport. Experimental proof for the existence of channels for charge transport was obtained by observing a photocurrent in a simple photovoltaic cell.

An intermolecular pyrene excimer in the pyrene-labeled N-thiophosphorylated thiourea and its nickel(ii) complex

(1-pyrene)NHC(S)NHP(S)(OiPr)₂ (HL) and its Ni^II complex ([NiL2]) have been synthesized. Both HL and [NiL2] were found to be emissive in solution of CH₂Cl₂, which is due to the concentration dependent emission of the pyrene monomer and excimer.

Metal ion influences distortion of the ligand in the structure of [M{2-MeO(O)CC6H4NHC(S)NP(S)(OiPr)2}2] (M = Zn(II), Cd(II)) complexes: a driving force for intermolecular aggregation

Reaction of the in situ deprotonated N-thiophosphorylated thiourea 2-MeO(O)CC6H4NHC(S)NHP(S)(OiPr)2 () with MCl2 (M = Zn(II), Cd(II)) in aqueous ethanol leads to complexes of the formula . Both compounds crystallise in the triclinic space group P1[combining macron] with Z = 2 and the metal cations are found in a tetrahedral S2S coordination environment formed by the C-S and P-S sulfur atoms. The crystal structures reveal intramolecular N-HO[double bond, length as m-dash]C hydrogen bonds formed within the 2-MeO(O)CC6H4NH fragments. Both structures are further stabilised by intermolecular ππ stacking interactions, which are more efficient in . Here, a pronounced dimeric intermolecular aggregate is observed which goes along with a pronounced distortion of the chelate [(S)CNP(S)](-) backbone of the ligand upon coordination to Cd(II) as well as a significantly distorted coordination tetrahedron CdS2S. The aggregation is also reflected in the positive electrospray ionisation (ESI) mass spectrum of the Cd(II) complex, which exhibits peaks for the dimeric cations [Cd2L3](+), [Cd2L4 + H](+) and [Cd2L4 + Na](+), while for the Zn(II) analogue only monomeric species were observed. Quantum chemical ETS-NOCV (ADF) calculations confirm the higher stability of dimers in compared with . The ππ stacking interactions are prodominantly due to dispersion contributions, though the electrostatic and orbital interaction components are also important. QTAIM (ADF) type calculations additionally quantify the covalent and non-covalent interactions in the momomers.

Ratiometric sensing of lysine through the formation of the pyrene excimer: experimental and computational studies

Lysine assisted ratiometric monomer to excimer conversion of pyrene derivatives allows intracellular lysine detections.

Enthalpy–entropy relations in the acid–base equilibrium of warfarin and 10-hydroxywarfarin; joint experimental and theoretical studies

Warfarin and 10-hydroxywarfarin are structurally similar molecules, however, they exhibit considerably different thermodynamics of acid dissociation. Intramolecular H-bonds and solvent composition are the factors of great importance.

Mapping environmental partitioning properties of nonpolar complex mixtures by use of GC × GC

Comprehensive two-dimensional gas chromatography (GC × GC) is effective for separating and quantifying nonpolar organic chemicals in complex mixtures. Here we present a model to estimate 11 environmental partitioning properties for nonpolar analytes based on GC × GC chromatogram retention time information. The considered partitioning properties span several phases including pure liquid, air, water, octanol, hexadecane, particle natural organic matter, dissolved organic matter, and organism lipids. The model training set and test sets are based on a literature compilation of 648 individual experimental partitioning property data. For a test set of 50 nonpolar environmental contaminants, predicted partition coefficients exhibit root-mean-squared errors ranging from 0.19 to 0.48 log unit, outperforming Abraham-type solvation models for the same chemical set. The approach is applicable to nonpolar organic chemicals containing C, H, F, Cl, Br, and I, having boiling points ≤402 °C. The presented model is calibrated, easy to apply, and requires the user only to identify a small set of known analytes that adapt the model to the GC × GC instrument program. The analyst can thus map partitioning property estimates onto GC × GC chromatograms of complex mixtures. For example, analyzed nonpolar chemicals can be screened for long-range transport potential, aquatic bioaccumulation potential, arctic contamination potential, and other characteristic partitioning behaviors.

Forced bonding and QTAIM deficiencies: a case study of the nature of interactions in He@adamantane and the origin of the high metastability

Calculations within the framework of the interacting quantum atoms (IQA) approach have shown that the interactions of the helium atom with both tertiary, tC, and secondary, sC, carbon atoms in the metastable He@adamantane (He@adam) endohedral complex are bonding in nature, whereas the earlier study performed within the framework of Bader's quantum theory of atoms in molecules (QTAIM) revealed that only He---tC interactions are bonding. The He---tC and He---sC bonding interactions are shown to be forced by the high pressure that the helium and carbon atoms exert upon each other in He@adam. The occurrence of a bonding interaction between the helium and sC atoms, which are not linked by a bond path, clearly shows that the lack of a bond path between two atoms does not necessarily indicate the lack of a bonding interaction, as is asserted by QTAIM. IQA calculations showed that not only the destabilization of the adamantane cage, but also a huge internal destabilization of the helium atom, contribute to the metastability of He@adam, these contributions being roughly equal. This result disproves previous opinions based on QTAIM analysis that only the destabilization of the adamantane cage accounts for the endothermicity of He@adam. Also, it was found that there is no homeomorphism of the ρ(r) and -v(r) fields of He@adam. Comparison of the IQA and QTAIM results on the interactions in He@adam exposes other deficiencies of the QTAIM approach. The reasons for the deficiencies in the QTAIM approach are analyzed.

The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: database survey and computational studies

Database survey in this study revealed that about one-third of the protein structures deposited in the Protein Data Bank (PDB) contain arginine-arginine (Arg-Arg) pairing with a carbon···carbon (CZ···CZ) interaction distance less than 5 Å. All the Arg-Arg pairings were found to bury in a polar environment composed of acidic residues, water molecules, and strong polarizable or negatively charged moieties from binding site or bound ligand. Most of the Arg-Arg pairings are solvent exposed and 68.3% Arg-Arg pairings are stabilized by acidic residues, forming Arg-Arg-Asp/Glu clusters. Density functional theory (DFT) was then employed to study the effect of environment on the pairing structures. It was revealed that Arg-Arg pairings become thermodynamically stable (about -1 kcal/mol) as the dielectric constant increases to 46.8 (DMSO), in good agreement with the results of the PDB survey. DFT calculations also demonstrated that perpendicular Arg-Arg pairing structures are favorable in low dielectric constant environment, while in high dielectric constant environment parallel structures are favorable. Additionally, the acidic residues can stabilize the Arg-Arg pairing structures to a large degree. Energy decomposition analysis of Arg-Arg pairings and Arg-Arg-Asp/Glu clusters showed that both solvation and electrostatic energies contribute significantly to their stability. The results reported herein should be very helpful for understanding Arg-Arg pairing and its application in drug design.