The Nature of Interactions in the Ionic Crystal of 3-Pentenenitrile, 2-Nitro-5-oxo, Ion(−1), Sodium

σ-Hole Bonds and the VSEPR Model—From the Tetrahedral Structure to the Trigonal Bipyramid

Complexes linked by various interactions are analysed in this study. They are characterized by the tetrahedral configuration of the Lewis acid centre. Interactions, being a subject of this study, are classified as σ-hole bonds, such as the halogen, chalcogen, pnicogen, and tetrel bonds. In the case of strong interactions, the tetrahedral configuration of the Lewis acid centre changes into the trigonal bipyramid configuration. This change is in line with the Valence-Shell Electron-Pair Repulsion model, VSEPR, and this is supported here by the results of high-level ab initio calculations. The theoretical results concerning the geometries are supported mainly by the Natural Bond Orbital, NBO, method.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

Revisiting the halogen bonding between phosphodiesterase type 5 and its inhibitors

Halogenated ligands are nowadays commonly designed in order to increase their potency against protein targets. Although novel computational methods of evaluating the affinity of such halogenated inhibitors have emerged, they still lack the sufficient accuracy, which is especially noticeable in the case of empirical scoring functions, being the method of choice in the drug design process. Here, we evaluated a series of halogenated inhibitors of phosphodiesterase type 5 with ab initio methods, revealing the physical nature of ligand binding and determining the components of interaction energy that are essential for proper inhibitor ranking. In particular, a nonempirical scoring model combining long-range contributions to the interaction energy provided a significant correlation with experimental binding potency, outperforming a number of commonly used empirical scoring functions. Considering the low computational cost associated with remarkable predictive abilities of the aforementioned model, it could be used for rapid assessment of the ligand affinity in the process of rational design of novel halogenated compounds.

Theoretical Model of EphA2-Ephrin A1 Inhibition

This work aims at the theoretical description of EphA2-ephrin A1 inhibition by small molecules. Recently proposed ab initio-based scoring models, comprising long-range components of interaction energy, is tested on lithocholic acid class inhibitors of this protein–protein interaction (PPI) against common empirical descriptors. We show that, although limited to compounds with similar solvation energy, the ab initio model is able to rank the set of selected inhibitors more effectively than empirical scoring functions, aiding the design of novel compounds.

Interactions of Substituted Nitroaromatics with Model Graphene Systems: Applicability of Hammett Substituent Constants To Predict Binding Energies

Applicability of Hammett parameters (σ m and σ p ) was tested in extended π-systems in gas phase. Three different model graphene systems, viz. 5,5-graphene (GR), 3-B-5,5-graphene (3BGR), and 3-N-5,5-graphene (3NGR), were designed as extended π-systems, and interactions of various nitrobenzene derivatives (mainly m- and p-substituted together with some multiple substitutions) on such platforms were monitored using density functional theory (M06/cc-pVDZ, M06/cc-pVTZ, M06/sp-aug-cc-pVTZ) and Møller-Plesset second-order perturbation (MP2/cc-pV-DZ) theory. Offset face to face (OSFF) stackings were found to be the favored orientations, and reasonable correlations were found between binding energies (ΔE B) and the ∑|σ m | values of the substituted nitrobenzenes. It was proposed previously that |σ m | contains information about the substituents' polarizability and controls electrostatic and dispersion interactions. The combination of ∑|σ m | and molar refractivity (as ∑M r) or change in polarizability (Δα: with respect to benzene) of nitrobenzene derivatives generated statistically significant correlation with respect to ΔE B, thereby supporting the hypothesis related to the validity of |σ m | correlations. The |σ p | parameters also maintain similar correlations for the various p-substituted nitrobenzene derivatives together with several multiply-substituted nitrobenzene derivatives. The correlation properties in such cases are similar to the |σ m | cases, and the energy partition analysis for both the situations reveled importance of electrostatic and dispersion contributions in such interactions. The applicability of Hammett parameters was observed previously on the restricted parallel face to face orientation of benzene···substituted benzene systems, and the present results show that such an idea could be used to predict ΔE B values in OSFF orientations, if the scaffolds are designed in such a way that substituted benzene systems cannot escape their π-clouds.

Theoretical models of inhibitory activity for inhibitors of protein-protein interactions: targeting menin-mixed lineage leukemia with small molecules

A computationally affordable, non-empirical model based on electrostatic multipole and dispersion terms successfully predicts the binding affinity of inhibitors of menin–MLL protein–protein interactions.

Development and binding affinity predictions of inhibitors targeting protein–protein interactions (PPI) still represent a major challenge in drug discovery efforts. This work reports application of a predictive non-empirical model of inhibitory activity for PPI inhibitors, exemplified here for small molecules targeting the menin–mixed lineage leukemia (MLL) interaction. Systematic ab initio analysis of menin–inhibitor complexes was performed, revealing the physical nature of these interactions. Notably, the non-empirical protein–ligand interaction energy comprising electrostatic multipole and approximate dispersion terms (E(10)El,MTP + E_Das) produced a remarkable correlation with experimentally measured inhibitory activities and enabled accurate activity prediction for new menin–MLL inhibitors. Importantly, this relatively simple and computationally affordable non-empirical interaction energy model outperformed binding affinity predictions derived from commonly used empirical scoring functions. This study demonstrates high relevance of the non-empirical model we developed for binding affinity prediction of inhibitors targeting protein–protein interactions that are difficult to predict using empirical scoring functions.

Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition

There is a need for improved and generally applicable scoring functions for fragment-based approaches to ligand design. Here, we evaluate the performance of a computationally efficient model for inhibitory activity estimation, which is composed only of multipole electrostatic energy and dispersion energy terms that approximate long-range ab initio quantum mechanical interaction energies. We find that computed energies correlate well with inhibitory activity for a compound series with varying substituents targeting two subpockets of the binding site of Trypanosoma brucei pteridine reductase 1. For one subpocket, we find that the model is more predictive for inhibitory activity than the ab initio interaction energy calculated at the MP2 level. Furthermore, the model is found to outperform a commonly used empirical scoring method. Finally, we show that the results for the two subpockets can be combined, which suggests that this simple nonempirical scoring function could be applied in fragment–based drug design.

Hydrogen bonds, and σ-hole and π-hole bonds – mechanisms protecting doublet and octet electron structures

For various interactions electron charge shifts try to protect the former doublet or octet electronic structure of the Lewis acid centre.

Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method

Vibrational solvatochromism is a solvation-induced effect on fundamental vibrational frequencies of molecules in solutions. Here we present a detailed first-principle coarse-grained theory of vibrational solvatochromism, which is an extension of our previous work [B. Błasiak, H. Lee, and M. Cho, J. Chem. Phys. 139(4), 044111 (2013)] by taking into account electrostatic, exchange-repulsion, polarization, and charge-transfer interactions. By applying our theory to the model N-methylacetamide-water clusters, solute-solvent interaction-induced effects on amide I vibrational frequency are fully elucidated at Hartree-Fock level. Although the electrostatic interaction between distributed multipole moments of solute and solvent molecules plays the dominant role, the contributions from exchange repulsion and induced dipole-electric field interactions are found to be of comparable importance in short distance range, whereas the charge-transfer effect is negligible. The overall frequency shifts calculated by taking into account the contributions of electrostatics, exchange-repulsion, and polarization terms are in quantitative agreement with ab initio results obtained at the Hartree-Fock level of theory.

Physical Nature of Fatty Acid Amide Hydrolase Interactions with Its Inhibitors: Testing a Simple Nonempirical Scoring Model

Fatty acid amide hydrolase (FAAH) is an enzyme responsible for the deactivating hydrolysis of fatty acid ethanolamide neuromodulators. FAAH inhibitors have gained considerable interest due to their possible application in the treatment of anxiety, inflammation, and pain. In the context of inhibitor design, the availability of reliable computational tools for predicting binding affinity is still a challenging task, and it is now well understood that empirical scoring functions have several limitations that in principle could be overcome by quantum mechanics. Herein, systematic ab initio analyses of FAAH interactions with a series of inhibitors belonging to the class of the N-alkylcarbamic acid aryl esters have been performed. In contrast to our earlier studies of other classes of enzyme-inhibitor complexes, reasonable correlation with experimental results required us to consider correlation effects along with electrostatic term. Therefore, the simplest comprehensive nonempirical model allowing for qualitative predictions of binding affinities for FAAH ligands consists of electrostatic multipole and second-order dispersion terms. Such a model has been validated against the relative stabilities of the benchmark S66 set of biomolecular complexes. As it does not involve parameters fitted to experimentally derived data, this model offers a unique opportunity for generally applicable inhibitor design and virtual screening.

A theoretical study on the stability and intramolecular interaction in 5-nitrotetrazolates with the DFT and DFT-D methods

Two new salts 3,5-diazido-1,2,4-triazolium 5-nitrotetrazolate and 1-methyl-3,5-diazido-1,2,4-triazolium 5-nitrotetrazolate were designed based on the structures of experimentally synthesized 3-azido-1,2,4-triazolium 5-nitro-tetrazolate and 1-methyl-3-azido-1,2,4-triazolium 5-nitro-tetrazolate, to explore new promising candidates for energetic materials and to investigate the influences of the substituents (- CH 3 and - N 3) and solvent (water) on the intramolecular interactions and properties. The intramolecular hydrogen bonding interactions were investigated by the natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) analyses using the density functional theory (DFT) and the dispersion correction DFT (DFT-D) methods. The low-lying singlet electronic transitions were estimated using the time-dependent DFT. All four examined salts exist as ionic structures in aqueous solution while acid–base molecular complexes form in gas phase. The hydrogen bond energy (E H ) obtained with the DFT-D method is larger than that obtained with the DFT method, but the trend is consistent, i.e. - N 3 increases while - CH 3 decreases E H . In addition, the position of the strongest electronic absorption peak has a little correlation with the number of - N 3 and - CH 3 groups. 3,5-diazido-1,2,4-triazolium 5-nitrotetrazolate is a valuable energetic salt with the highest nitrogen content, oxygen coefficient and density and the second highest heat of formation and chemical stability.

Computational studies of darunavir into HIV-1 protease and DMPC bilayer: necessary conditions for effective binding and the role of the flaps

Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the main targets toward AIDS therapy. We have selected the potent drug darunavir and a weak inhibitor (fullerene analog) as HIV-1 PR substrates to compare protease's conformational features upon binding. Molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and quantum-mechanical (QM) calculations indicated the importance of the stability of HIV-1 PR flaps toward effective binding: a weak inhibitor may induce flexibility to the flaps, which convert between closed and semiopen states. A water molecule in the darunavir-HIV-1 PR complex bridged the two flap tips of the protease through hydrogen bonding (HB) interactions in a stable structure, a feature that was not observed for the fullerene-HIV-1 PR complex. Additionally, despite that van der Waals interactions and nonpolar contribution to solvation favored permanent fullerene entrapment into the cavity, these interactions alone were not sufficient for effective binding; enhanced electrostatic interactions as observed in the darunavir-complex were the crucial component of the binding energy. An alternative pathway to the usual way of a ligand to access the cavity was also observed for both compounds. Each ligand entered the binding cavity through an opening between the one flap of the protease and a neighboring loop. This suggested that access to the cavity is not necessarily regulated by flap opening. Darunavir exerts its biological action inside the cell, after crossing the membrane barrier. Thus, we also initiated a study on the interactions between darunavir and the DMPC bilayer to reveal that the drug was accommodated inside the bilayer in conformations that resembled its structure into HIV-1 PR, being stabilized via HBs with the lipids and water molecules.

A quantum-chemical study of the binding ability of βXaaHisGlyHis towards copper(II) ion

The present study analyzed binding of Cu²⁺ to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches including electron correlation effects. In order to shed light on the character of interactions between Cu²⁺ and peptides, which are expected to be mainly electrostatic in nature, decomposition of interaction energy into physically meaningful components was applied.

Intriguing relations of interaction energy components in stacked nucleic acids

Major components of the interaction energy that define several approximate levels starting from second order Möller-Plesset theory were studied for 58 stacked nucleic acid dimers. They included typical B-DNA and A-DNA structures, and selected published geometries. A survey of the various terms yields an unexpected correlation between the Pauli exchange and dispersion or correlation terms, which holds for each class of similar planar geometries and for various basis sets. The geometries that exhibit these correlations span a specific range of molecular overlaps when compared to a model benzene-pyridine stacked dimer. Also, the relationship between electrostatic interactions and MP2 stabilization energies reported earlier is confirmed and a prediction interval of practical relevance is estimated.

Structures of the Intermediates Formed in the Ring-Opening Reaction of 2-Chloro-3-nitropyridine

The reaction of 2-chloro-3-nitropyridine with two equivalents of hydroxide ion was studied by NMR and X-ray crystallography. On the basis of NMR coupling constants, the originally formed ring-opened intermediate is the pseudo-cis form, as predicted by the SN(ANRORC) mechanism. However, the first intermediate is unstable and isomerizes to a second intermediate, which was isolated. The pseudo-trans geometry of the second intermediate [3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium] explains why additional base does not lead to the ring-closing reaction as observed with 2-chloro-5-nitropyridine.

On the influence of microsolvation by argon atoms on the electron affinity properties of water dimer

This work provides a comparison of neutral (H2O)2Ar(n) and negatively charged (H2O)(2-)Ar(n) complexes. The excess electron stabilizes the complexes and leads to the trans to cis rearrangement within the water dimer core. In the case of small complexes (n < or = 4) the microsolvation of the dimer by argon atoms arises on the trans side with respect to the donor water molecule. The stabilization of an excess electron is enhanced by the delocalization of the electronic charge density due to microsolvation. The process of cis to trans rotation is induced by the electric field of the approaching negative charge. The interaction energy decomposition suggests a more ionic character of binding in the negatively charged complexes. The attachment of an electron is controlled by the correlation energy.