Noncovalent interactions in biochemistry

Effect of Lanthanide Ions and Triazole Ligands on the Molecular Properties, Spectroscopy and Pharmacological Activity

The effect of La, Ce, Pr and Nd ions on four Ln(ligand)3 complexes and at three DFT levels of calculation was analyzed. Four ligands were chosen, three of which were based on the 1,2,3-triazole ring. The DFT methods used were B3LYP, CAM-B3LYP and M06-2X. The relationships established were between the geometric parameters, atomic charges, HOMO-LUMO energies and other molecular properties. These comparisons and trends will facilitate the synthesis of new complexes by selecting the ligand and lanthanide ion best suited to the desired property of the complex. The experimental IR and Raman spectra of Ln(2b')3 complexes where Ln = La, Ce, Pr, Nd, Sm, Gd, Dy, Ho and Er ions have been recorded and compared to know the effect of the lanthanide ion on the complex. The hydration in these complexes was also analyzed. Additionally, the effect of the type of coordination center on the ability of an Ln(ligand)3 complex to participate in electron exchange and hydrogen transfer was investigated using two in vitro model systems-DPPH and ABTS.

Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments

Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides' structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster.

Base pairs with 5-chloroorotic acid and comparison with the natural nucleobase. Structural and spectroscopic study, and three suggested antiviral modified nucleosides

A structural and spectroscopic study of 5-chloroorotic acid (5-ClOA) biomolecule was carried out by IR and FT-Raman and the results obtained were compared to those achieved in 5-fluoroorotic acid and 5-aminoorotic acid compounds. The structures of all possible tautomeric forms were determined using DFT and MP2 methods. To know the tautomer form present in the solid state, the crystal unit cell was optimized through dimer and tetramer forms in several tautomeric forms. The keto form was confirmed through an accurate assignment of all the bands. For this purpose, an additional improvement in the theoretical spectra was carried out using linear scaling equations (LSE) and polynomic equations (PSE) deduced from uracil molecule. Base pairs with uracil, thymine and cytosine nucleobases were optimized and compared to the natural Watson-Crick (WC) pairs. The counterpoise (CP) corrected interaction energies of the base pairs were also calculated. Three nucleosides were optimized based on 5-ClOA as nucleobase, and their corresponding WC pairs with adenosine. These modified nucleosides were inserted in DNA:DNA and RNA:RNA microhelices, which were optimized. The position of the -COOH group in the uracil ring of these microhelices interrupts the DNA/RNA helix formation. Because of the special characteristic of these molecules they can be used as antiviral drugs.Communicated by Ramaswamy H. Sarma.

Iodinated 4,4'-Bipyridines with Antiproliferative Activity Against Melanoma Cell Lines

In the last decade, biological processes involving halogen bond (HaB) as a leading interaction attracted great interest. However, although bound iodine atoms are considered powerful HaB donors, few iodinated new drugs were reported so far. Recently, iodinated 4,4'-bipyridines showed interesting properties as HaB donors in solution and in the solid state. In this paper, a study on the inhibition activity of seven halogenated 4,4'-bipyridines against malignant melanoma (MM) cell proliferation is described. Explorative dose/response proliferation assays were first performed with three 4,4'-bipyridines by using four MM cell lines and the normal BJ fibroblast cell line as control. Among them, the A375 MM cell line was the most sensitive, as determined by MTT assays, which was selected to evaluate the antiproliferative activity of all 4,4'-bipyridines. Significantly, the presence of an electrophilic iodine impacted the biological activity of the corresponding compounds. The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine showed significant antiproliferation activity against the A375 cell line, and lower toxicity on BJ fibroblasts. Through in silico studies, the stereoelectronic features of possible sites determining the bioactivity were explored. These results pave the way for the utilization of iodinated 4,4'-bipyridines as templates to design new promising HaB-enabled inhibitors of MM cell proliferation.

Femtosecond Collisional Dissipation of Vibrating D_{2}^{+} in Helium Nanodroplets

We explored the collision-induced vibrational decoherence of singly ionized D_{2} molecules inside a helium nanodroplet. By using the pump-probe reaction microscopy with few-cycle laser pulses, we captured in real time the collision-induced ultrafast dissipation of vibrational nuclear wave packet dynamics of D_{2}^{+} ion embedded in the droplet. Because of the strong coupling of excited molecular cations with the surrounding solvent, the vibrational coherence of D_{2}^{+} in the droplet interior only lasts for a few vibrational periods and completely collapses within 140 fs. The observed ultrafast coherence loss is distinct from that of isolated D_{2}^{+} in the gas phase, where the vibrational coherence persists for a long time with periodic quantum revivals. Our findings underscore the crucial role of ultrafast collisional dissipation in shaping the molecular decoherence and solvation dynamics during solution chemical reactions, particularly when the solute molecules are predominantly in ionic states.

σ-Hole Site-Based Interactions within Hypervalent Pnicogen, Halogen, and Aerogen-Bearing Molecules with Lewis Bases: A Comparative Study

σ-Hole site-based interactions in the trigonal bipyramidal geometrical structure of hypervalent pnicogen, halogen, and aerogen-bearing molecules with pyridine and NCH Lewis bases (LBs) were comparatively examined. In this respect, the ZF5···, XF3O2···, and AeF2O3···LB complexes (where Z = As, Sb; X = Br, I; Ae = Kr, Xe; and LB = pyridine and NCH) were investigated. The electrostatic potential (EP) analysis affirmations outlined the occurrence of σ-holes on the systems under consideration with disparate magnitudes that increased according to the following order: AeF2O3 < XF3O2 < ZF5. In line with EP outcomes, the proficiency of σ-hole site-based interactions increased as the atomic size of the central atom increased with a higher favorability for the pyridine-based complexes over NCH-based ones. The interaction energy showed the most favorable negative values of -35.97, -44.53, and -56.06 kcal/mol for the XeF2O3···, IF3O2···, and SbF5···pyridine complexes, respectively. The preferentiality pattern of the studied interactions could be explained as a consequence of (i) the dramatic rearrangement of ZF5 molecules from the trigonal bipyramid geometry to the square pyramidal one, (ii) the significant and tiny deformation energy in the case of the interaction of XF3O2 molecules with pyridine and NCH, respectively, and (iii) the absence of geometrical deformation within the AeF2O3···pyridine and ···NCH complexes other than the XeF2O3···pyridine one. Quantum theory of atoms in molecules and noncovalent interaction index findings reveal the partially covalent nature of most of the investigated interactions. Symmetry-adapted perturbation theory affirmations declared that the electrostatic component was the driving force beyond the occurrence of the considered interactions. The obtained findings will help in improving our understanding of the effect of geometrical deformation on intermolecular interactions.

Magnetic Resonance-Based Analytical Tools to Study Polyvinylpyrrolidone-Hydroxyapatite Composites

The synthesis of biocompatible and bioresorbable composite materials, such as a "polymer matrix-mineral constituent," stimulating the natural growth of living tissues and the restoration of damaged parts of the body, is one of the challenging problems in regenerative medicine and materials science. Composite films of bioresorbable polymer of polyvinylpyrrolidone (PVP) and hydroxyapatite (HA) were obtained. HA was synthesized in situ in the polymer solution. We applied electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) approaches to study the composite films' properties. The application of EPR in two frequency ranges allowed us to derive spectroscopic parameters of the nitrogen-based light and radiation-induced paramagnetic centers in HA, PVP and PVP-HA with high accuracy. It was shown that PVP did not significantly affect the EPR spectral and relaxation parameters of the radiation-induced paramagnetic centers in HA, while light-induced centers were detected only in PVP. Magic angle spinning (MAS) 1H NMR showed the presence of two signals at 4.7 ppm and -2.15 ppm, attributed to "free" water and hydroxyl groups, while the single line was attributed to 31P. NMR relaxation measurements for 1H and 31P showed that the relaxation decays were multicomponent processes that can be described by three components of the transverse relaxation times. The obtained results demonstrated that the applied magnetic resonance methods can be used for the quality control of PVP-HA composites and, potentially, for the development of analytical tools to follow the processes of sample treatment, resorption, and degradation.

Structural Study of a La(III) Complex of a 1,2,3-Triazole Ligand with Antioxidant Activity

The 1,2,3-triazole derivative 2-(4-chlorophenyl)-5-(pyrrolidin-1-yl)-2H-1,2,3-triazole-4-carboxylic acid with potential anticancer activity was used as a ligand in complex formation with the lanthanum(III) ion. The molecular structure and vibrational spectra of the complex were optimized at three DFT levels, and the scaled IR and Raman spectra were compared to the experimental ones. Several scaling procedures were used. Through a detailed analysis, the structure predicted for the newly synthetized La(III) complex was confirmed by the good accordance of the calculated/experimental IR and Raman spectra. The best DFT method appeared to be M06-2X with the Lanl2mb basis set, followed closely by Lanl2dz. The effect of the lanthanide atom on the molecular structure and atomic charge distribution of the triazole ring was evaluated. The potential free radical scavenging activity of both the ligand and the complex was investigated in several radical-generating model systems. The potential mechanisms of antioxidant action (hydrogen atom transfer (HAT) and single-electron transfer (SET)) were elucidated.

Regularized and Opposite Spin-Scaled Functionals from Møller-Plesset Adiabatic Connection─Higher Accuracy at Lower Cost

Noncovalent interactions (NCIs) play a crucial role in biology, chemistry, material science, and everything in between. To improve pure quantum-chemical simulations of NCIs, we propose a methodology for constructing approximate correlation energies by combining an interpolation along the Møller-Plesset adiabatic connection (MP AC) with a regularization and spin-scaling strategy applied to MP2 correlation energies. This combination yields cosκos-SPL2, which exhibits superior accuracy for NCIs compared to any of the individual strategies. With the N4 formal scaling, cosκos-SPL2 is competitive or often outperforms more expensive dispersion-corrected double hybrids for NCIs. The accuracy of cosκos-SPL2 particularly shines for anionic halogen bonded complexes, where it surpasses standard dispersion-corrected DFT by a factor of 3 to 5.

The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems

It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.

Efficient Calculation of the Dispersion Energy for Multireference Systems with Cholesky Decomposition: Application to Excited-State Interactions

Accurate and efficient prediction of dispersion interactions in excited-state complexes poses a challenge due to the complex nature of electron correlation effects that need to be simultaneously considered. We propose an algorithm for computing the dispersion energy in nondegenerate ground- or excited-state complexes with arbitrary spin. The algorithm scales with the fifth power of the system size due to employing Cholesky decomposition of Coulomb integrals and a recently developed recursive formula for density response functions of the monomers. As a numerical illustration, we apply the new algorithm in the framework of multiconfigurational symmetry adapted perturbation theory, SAPT(MC), to study interactions in dimers with localized excitons. The SAPT(MC) analysis reveals that the dispersion energy may be the main force stabilizing excited-state dimers.

Interactions between Paracetamol and Formaldehyde: Theoretical Investigation and Topological Analysis

In this work, noncovalent interactions including hydrogen bonds, C···C, N···O, and van der Waals forces between paracetamol and formaldehyde were investigated using the second-order perturbation theory MP2 in conjunction with the correlation consistent basis sets (aug-cc-pVDZ and aug-cc-pVTZ). Two molecular conformations of paracetamol were considered. Seven equilibrium geometries of dimers were found from the result of the interactions with formaldehyde for each conformation of paracetamol. Interaction energies of complexes with both ZPE and BSSE corrections range from -7.0 to -21.7 kJ mol^-1. Topological parameters (such as electron density, its Laplacian, and local electron energy density at the bond critical points) of the bonds from atoms in molecules theory were analyzed in detail. The natural bond orbital analysis showed that the stability of complexes was controlled by noncovalent interactions including O-H···O, N-H···O, C-H···O, C-H···N, C-H···H-C, C···C, and N···O. The red- and blue-shifted hydrogen bonds could both be observed in these complexes. The properties of these interactions were also further examined in water using a polarized continuum model. In water, the stability of the complex was slightly reduced as compared to that in the gas phase.

Dispersion Energy from the Time-Independent Coupled-Cluster Polarization Propagator

We present a new method of calculation of the dispersion energy in the second-order symmetry-adapted perturbation theory. Using the Longuet-Higgins integral and time-independent coupled-cluster response theory, one shows that the general expression for the dispersion energy can be written in terms of cluster amplitudes and the excitation operators σ, which can be obtained by solving a linear equation. We introduced an approximate scheme dubbed CCPP2(T) for the dispersion energy accurate to the second order of intramonomer correlation, which includes certain classes to be summed to infinity. Assessment of the accuracy of the CCPP2(T) dispersion energy against the FCI dispersion for He₂ demonstrates its high accuracy. For more complex systems, CCPP2(T) matches the accuracy of the best methods introduced for calculations of dispersion so far. The method can be extended to higher-order levels of excitations, providing a systematically improvable theory of dispersion interaction.

How proton transfer affects the helical parameters in DNA:DNA microhelices

Proton transfer reactions are a widespread phenomenon in many areas of the life sciences and it is one of the origins of the spontaneous point mutations during DNA replication. Because of its importance, many studies have been reported on these reactions. However, the present work is the first one focused on the structural geometrical changes by double proton transfer (DPT). Thus, different Watson-Crick (WC) pairs were optimized first in a simple model with one nucleoside base pair, and in a microhelix form with three nucleoside base pairs. The canonical and few tautomeric forms were considered in DNA:DNA microhelices with A-type and B-type helical forms. The stability of these structures and how the DPT process affects the main geometrical parameters was analyzed, in particular the deformation of the helical parameters. The M06-2X DFT method was used for this purpose. The purine/pyrimidine ring in the keto form appears easier to be deformed than when it is in the enol form. The weaker WC base pair formed with mixed microhelices than with nucleobases alone and the significant deformation of the helical and backbone parameters with the DPT appears to complicate this process in microhelices.Communicated by Ramaswamy H. Sarma.

Structures of the (Imidazole)nH+ ... Ar (n=1,2,3) complexes determined from IR spectroscopy and quantum chemical calculations

Here, we present new cryogenic infrared spectra of the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + (n=1,2,3) ions. The data was obtained using helium tagging infrared predissociation spectroscopy. The new results were compared with the data obtained by Gerardi et al. (Chem. Phys. Lett. 501:172–178, 2011) using the same technique but with argon as a tag. Comparison of the two experiments, assisted by theoretical calculations, allowed us to evaluate the preferable attachment positions of argon to the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + frame. Argon attaches to nitrogen-bonded hydrogen in the case of the (Imidazole)H$$^+$$ + ion, while in (Imidazole)$$_{2}\mathrm{H}^{+}$$ 2 H + and (Imidazole)$$_{3}\mathrm{H}^{+}$$ 3 H + the preferred docking sites for the argon are in the center of the complex. This conclusion is supported by analyzing the spectral features attributed to the N–H stretching vibrations. Symmetry adapted perturbation theory (SAPT) analysis of the non-covalent forces between argon and the (Imidazole)$$_{n}\mathrm{H}^{+}$$ n H + (n=1,2,3) frame revealed that this switch of docking preference with increasing complex size is caused by an interplay between induction and dispersion interactions.

Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems

Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.

Mussel‐Inspired Biomaterials: From Chemistry to Clinic

After several billions of years, nature still makes decisions on its own to identify, develop, and direct the most effective material for phenomena/challenges faced. Likewise, and inspired by the nature, we learned how to take steps in developing new technologies and materials innovations. Wet and strong adhesion by Mytilidae mussels (among which Mytilus edulis—blue mussel and Mytilus californianus—California mussel are the most well‐known species) has been an inspiration in developing advanced adhesives for the moist condition. The wet adhesion phenomenon is significant in designing tissue adhesives and surgical sealants. However, a deep understanding of engaged chemical moieties, microenvironmental conditions of secreted proteins, and other contributing mechanisms for outstanding wet adhesion mussels are essential for the optimal design of wet glues. In this review, all aspects of wet adhesion of Mytilidae mussels, as well as different strategies needed for designing and fabricating wet adhesives are discussed from a chemistry point of view. Developed muscle‐inspired chemistry is a versatile technique when designing not only wet adhesive, but also, in several more applications, especially in the bioengineering area. The applications of muscle‐inspired biomaterials in various medical applications are summarized for future developments in the field.

Probing Noncovalent Interactions in [3,3]Metaparacyclophanes

Arene-arene interactions are fundamentally important in molecular recognition. To precisely probe arene-arene interactions in cyclophanes, we designed and synthesized (2,6-phenol)paracyclophanes and (2,6-aniline)paracyclophanes that possess two aromatic rings in close proximity. Fine-tuning the aromatic character of one aromatic ring by fluorine substituents enables investigations on the intramolecular interactions between the electron-rich phenol and aniline with tetra-H- and tetra-F-substituted benzene. pK_a measurements revealed that the tetra-F-template increases the acidity of the phenol (ΔpK_a = 0.55). X-ray crystallography and computational analyses demonstrated that all [3,3]metaparacyclophanes adopt cofacial parallel conformations, implying the presence of π-π stacking interactions. Advanced quantum chemical analyses furthermore revealed that both electrostatic interactions and orbital interactions provide the key contribution to the structure and stability of [3,3]metaparacyclophanes.

Investigation of the Nature of Intermolecular Interactions in Tetra(thiocyanato)corrolato-Ag(III) Complexes: Agostic or Hydrogen Bonded?

Tetra(thiocyanato)corrolato-Ag(III) complexes presented here constitute a new class of metallo-corrole complexes. The spectroscopic properties of these complexes are quite unusual and interesting. For example, the absorption spectra of these β-substituted corrolato-Ag(III) complexes are very different from those of the β-unsubstituted corrolato-Ag(III) derivatives. Single-crystal XRD analysis of a representative tetra(thiocyanato)corrolato-Ag(III) derivative reveals C-H···Ag interactions. The C-H···Ag interactions are rarely demonstrated in the crystal lattice of a discrete coordination/organometallic compound. Optimization of the hydrogen positions of the crystal structure discloses the geometrical parameters of the said interaction as a Ag···H distance of 2.597 Å and ∠C-H···Ag of 109.62°. The natural bond orbital analysis provides information about the donor-acceptor orbitals involved in the interactions and their interaction energies. It was observed that the σ_C-H orbital overlaps with the vacant d-orbital of Ag with an interaction energy of 17.93 kJ/mol. The filled d-orbital of Ag overlaps with the σ*_C-H orbital with an interaction energy of 4.79 kJ/mol. The highlights of this work are that the H···Ag distance is outside of the distance range for the typical agostic interaction but fitted with the weak H-bond distance. However, the ∠C-H···Ag angle is within the range of the agostic interaction. Both crystallographic data and electronic structure calculations reveal that these kinds of intermolecular interactions in square-planar d⁸ Ag(III) complexes are intermediate in nature. Thus, they cannot be categorically called either hydrogen bonding or agostic interaction.

Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials

Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.

Assessing the persistence of chalcogen bonds in solution with neural network potentials

Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what are the most prevalent non-covalent interactions occurring in a solute-Cl$^-$-THF mixture. The simulations in explicit solvent highlight competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.

The Role of Hydrogen Bonds in Interactions between [PdCl4]2- Dianions in Crystal

[PdCl₄]^2- dianions are oriented within a crystal in such a way that a Cl of one unit approaches the Pd of another from directly above. Quantum calculations find this interaction to be highly repulsive with a large positive interaction energy. The placement of neutral ligands in their vicinity reduces the repulsion, but the interaction remains highly endothermic. When the ligands acquire a unit positive charge, the electrostatic component and the full interaction energy become quite negative, signalling an exothermic association. Raising the charge on these counterions to +2 has little further stabilizing effect, and in fact reduces the electrostatic attraction. The ability of the counterions to promote the interaction is attributed in part to the H-bonds which they form with both dianions, acting as a sort of glue.

Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials

There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.

Malonaldehyde-like Systems: BeF2 Clusters—A Subtle Balance between Hydrogen Bonds, Beryllium Bonds, and Resonance

The stability of malonaldehyde is governed by intramolecular hydrogen bonds (IMHBs) as well as in malonaldehyde-like systems where oxygen is replaced by N or S at any of the basic sites. As beryllium bonds have been shown to strongly cooperate with hydrogen bonds, this work explores at the high level ab initio G4 level of theory the effect of including this non-covalent interaction in the system through its association with BeF2. Although malonaldehyde follows the expected trends, where the formation of a pseudocyclic form is favored also when IMHB and Be bonds are present, the subtle balance between both non-covalent interactions leads to some surprising results when other heteroatoms are involved, to the point that interaction energies can be much larger than expected or even cyclization is not favored. A complete analysis using different computational tools gives an answer to those cases escaping the predictable trends.

The effect of midbond functions on interaction energies computed using MP2 and CCSD(T)

In this article we use MP2 and CCSD(T) calculations for the A24 and S66 data sets to explore how midbond functions can be used to generate cost effective counterpoise corrected supramolecular interaction energies of noncovalent complexes. We use the A24 data set to show that the primary role of midbond functions is not to approach the complete basis set limit, but rather to ensure a balanced description of the molecules and the interaction region (unrelated to the basis set superposition error). The need for balance is a consequence of using atom centered basis sets. In the complete basis set limit, the error will disappear, but reaching the complete basis set limit is not feasible beyond small systems. For S66 we investigate the need for increasing the number of midbond centers. Results show that adding a second midbond center increases the accuracy, but the effect is secondary to changing the atom centered basis set. Further, by comparing calculations using the 3s3p2d1f1g midbond set with using aug-cc-pVDZ and aug-cc-pVTZ as midbond sets, we see that the requirements for the midbond set to be effective, is not just that it contains diffuse functions, but also that high angular momentum functions are included. By comparing two approaches for placing midbond centers we show that results are not particularly sensitive to placement as long as the placement is reasonable.

Cooperative Effect of Noncovalent Interactions on Tetrel Bonding in Halogenated Silanes

Tetrel bond, a weak noncovalent interaction between the  σ -hole of a Group IV element (Silicon in our case) and the cloud of an electronegative element (Oxygen in our case) is the focus of current work. The percentage strengthening of tetrel bond has been investigated by optimising 16 binary complexes of halogenated silane and water of general formula SiX n H 4 - n  - H 2 O and 16 ternary complexes, of general formula NaX - SiX n H 4 - n  -H 2 O, where X =F, Cl, Br and I and n = 1, 2, 3 and 4 at various levels of theory defined within the formalism of density functional theory (DFT). With the addition of NaX, tetrel bond between Si and O in SiX n H 4 - n  - H 2 O gets strengthened up to 49%, owing to cooperativity effect exerted by hydrogen bonding between X and H in the ternary complex NaX - SiX n H 4 - n  - H 2 O. In the series of complexes studied here, overall stabilization due to cooperativity lies between 10 kJ/mol to 170 kJ/mol. This large extent of reinforcement due to cooperativity has never been showcased before. The exceptional stabilization and reinforcement owe its genesis to the transformation of the ternary complex into a cluster orchestrated by the H-bonding in most of the cases and covalent bonding in few of the cases.

S66x8 noncovalent interactions revisited: new benchmark and performance of composite localized coupled-cluster methods

The S66x8 noncovalent interactions benchmark has been re-evaluated at the “sterling silver” level. Against this, a selection of computationally more economical alternatives has been assayed, ranging from localized CC to double hybrids and SAPT(DFT).

junChS and junChS-F12 Models: Parameter-free Efficient yet Accurate Composite Schemes for Energies and Structures of Noncovalent Complexes

A recently developed model chemistry (denoted as junChS [Alessandrini, S.; et al. J. Chem. Theory Comput. 2020, 16, 988-1006]) has been extended to the employment of explicitly correlated (F12) methods. This led us to propose a family of effective, reliable, and parameter-free schemes for the computation of accurate interaction energies of molecular complexes ruled by noncovalent interactions. A thorough benchmark based on a wide range of interactions showed that the so-called junChS-F12 model, which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries, has an improved performance with respect to its conventional counterpart and outperforms well-known model chemistries. Without employing any empirical parameter and at an affordable computational cost, junChS-F12 reaches subchemical accuracy. Accurate characterizations of molecular complexes are usually limited to energetics. To take a step forward, the conventional and F12 composite schemes developed for interaction energies have been extended to structural determinations. A benchmark study demonstrated that the most effective option is to add MP2-F12 core-valence correlation corrections to fc-CCSD(T)-F12/jun-cc-pVTZ geometries without the need of recovering the basis set superposition error and the extrapolation to the complete basis set.

Theoretical Investigation of the 4,5-Dibromorodamine Methyl Ester (TH9402) Photosensitizer Used in Photodynamic Therapy: Photophysics, Reactions in the Excited State, and Interactions with DNA

Photosensitizer (PS) molecules play a critical role in photodynamic therapy of cancer and the understanding of the molecular mechanism involved in the photophysics of these compounds, and their reactions in the excited state are, therefore, of great interest for the development of this technique. In this article, the photophysics of the cationic PS 4,5-dibromorodamine methyl ester (TH9402), its electron- and energy-transfer reactions in the excited triplet state, with molecular oxygen, nitric oxide, guanosine-5'-monophosphate (GMP), and guanine, and the interaction with DNA were evaluated. Time-dependent density functional theory calculations at the TPSSh/Def2-TZVP//B3LYP/Def2-TZVP level of theory in water solution reveals that the PS has a bright S₁ state 2.33 eV above the ground state that produces a fluorescent rate constant of 5.40 × 10⁷ s^-1, calculated using Fermi's golden rule within a path integral formalism. Once excited to the bright state, the main intersystem crossing (ISC) channel involves the coupling with the T₂ state just below S₁ (S₁ → T₂ → T₁) with an overall ISC rate constant of 10.1 × 10⁷ s^-1, in good agreement with the experimental data. Excited-state reaction thermodynamics, computed at the M06-2X/Def2-TZVP//B3LYP/Def2-TZVP level of theory in water, showed that from all the excited-state electron-transfer reactions studied, only the transfer from GMP to the PS is thermodynamically favorable, independent of the protonation state of guanosine, which indicates a possible DNA photo-oxidation mechanism for the PS. Triplet-triplet energy-transfer reactions from TH9402 to molecular oxygen, producing reactive singlet oxygen, and to the deprotonated guanosine, producing ³GMP^2-, are also thermodynamically favorable, with ΔG = -2.0 and -24.0 kcal//mol, respectively. However, the energy transfer to the monoprotonated guanosine is not favorable, (ΔG = 36.1), suggesting that in the DNA double-strand environment, this energy-transfer process may not be observed. The results show that the PS can act through electron transfer and triplet-triplet energy-transfer reactions involved in mechanism types I and II in photodynamic therapy. Interactions of TH9402 with the d(AGACGTCT)₂ octanucleotide revealed that the PS can intercalate between the d(GpC)-d(CpG) base pairs in three different orientations and, upon intercalation, the π → π* transition of the PS shows a bathochromic shift up to 90 nm and up to 60% decrease in intensity. Interactions through groove binding showed a smaller bathochromic shift of 52.2 nm and a 56% decrease in intensity of the main transition band.

Arene-Perfluoroarene Interactions in Solution

A systematic study of arene-perfluoroarene interactions in solution is presented. Using a combination of NMR titration experiments, X-ray crystallography, and computational analysis, we analyze the effects of fluorination, substituents, ring size, and solvation on the arene-perfluoroarene interaction. We find that fluorination, extension of the π systems, and enhancement of solvent polarity greatly stabilize the stacking energy up to 3 orders of magnitude (K_a = <1 to 6000 M^-1), with the highest K_a achieved for the interaction of water-soluble variants of perfluoronaphthalene and anthracene in buffered D₂O (pD = 12). Combining computational and experimental results, we conclude that this impressive binding energy is a result of enthalpically favorable electrostatic and dispersion interactions as well as the entropically driven hydrophobic effect. The enhanced understanding of arene-perfluoroarene interactions in aqueous solution sets the stage for the implementation of this abiotic intermolecular interaction in biology and medicine.

Noncovalent Interactions from Models for the Møller-Plesset Adiabatic Connection

Given the omnipresence of noncovalent interactions (NCIs), their accurate simulations are of crucial importance across various scientific disciplines. Here we construct accurate models for the description of NCIs by an interpolation along the Møller-Plesset adiabatic connection (MP AC). Our interpolation approximates the correlation energy, by recovering MP2 at small coupling strengths and the correct large-coupling strength expansion of the MP AC, recently shown to be a functional of the Hartree-Fock density. Our models are size consistent for fragments with nondegenerate ground states, have the same cost as double hybrids, and require no dispersion corrections to capture NCIs accurately. These interpolations greatly reduce large MP2 errors for typical π-stacking complexes (e.g., benzene-pyridine dimers) and for the L7 data set. They are also competitive with state-of-the-art dispersion enhanced functionals and can even significantly outperform them for a variety of data sets, such as CT7 and L7.

Target identification of a novel unsymmetrical 1,3,4-oxadiazole derivative with antiproliferative properties

1,3,4-Oxadiazole derivatives are widely used in research on antineoplastic drugs. Recently, we discovered a novel unsymmetrical 1,3,4-oxadiazole compound with antiproliferative properties called 2j. To further investigate its possible targets and molecular mechanisms, RNA-seq was performed and the differentially expressed genes (DEGs) were obtained after treatment. Data were analyzed using functional (Gene Ontology term) and pathway (Kyoto Encyclopedia of Genes and Genomes) enrichment of the DEGs. The hub genes were determined by the analysis of protein-protein interaction networks. The connectivity map (CMap) information provided insight into the model action of antitumor small molecule drugs. Hub genes have been identified through function gene networks using STRING analysis. The small molecular targets obtained by CMap comparison showed that 2j is a tubulin inhibitor and it acts mainly affecting tumor cells through the cell cycle, FoxO signaling pathway, apoptotic, and p53 signaling pathways. The possible targets of 2j could be TUBA1A and TUBA4A. Molecular docking results indicated that 2j interacts at the colchicine-binding site on tubulin.

Experimental and Theoretical Studies of Dimers Stabilized by Two Chalcogen Bonds in the Presence of a N···N Pnicogen Bond

The structure of the 5,6-dichloro-2,1,3-benzoselenadiazole homodimer, obtained by adding the ligand, 4,5-dichloro-o-phenylenediamine, to the methanolic solution of SeCl₄, was determined by X-ray crystallography, augmented by Fourier transform infrared, Raman, and NMR spectroscopy. The binding motif involves a pair of Se···N chalcogen bonds, with a supplementary N···N pnicogen bond. Quantum calculations provide assessments of the strengths of the individual interactions as well as their contributing factors. All together, these three bonds compose a total interaction energy between 5.4 and 16.8 kcal/mol, with the larger chalcogen atom associated with the strongest interactions. Replacement of the Se atoms by S and Te analogues allows analysis of the dependence of these forces on the nature of the chalcogen atom. Calculations also measure the importance to the binding of the presence of a second N atom on each diazole unit as well as the substituted phenyl ring to which it is fused.

Research of weak interaction between water and different monolayer graphene systems

Weak interactions play a very important role in the fields of supramolecular chemistry, molecular physics, materials science, etc. They have a great impact on the structure of the compounds in the gas, liquid and solid phases and the mechanism of some reaction processes. In this study, we visualized the intermolecular interactions between H₂O and different graphene systems through density functional theory. Because the surface of Graphene oxide (GO) has epoxy groups, hydroxyl groups, and other oxygen-containing groups. These groups are prone to hydrogen bonding with hydrogen atoms of H₂O, and we further explain some of them based on the acid-base theory. Also, we obtained the components of interactions between different graphene complex and H₂O by energy decomposition. Then we found that for systems with moderate strength hydrogen bonding, such as hydroxyl functional group systems, electrostatic attraction is dominant while the dispersion attraction and induction function play an auxiliary role together.

Differences in Interactions Within Viral Replication Complexes of SARS-CoV-2 (COVID-19) and SARS-CoV Coronaviruses Control RNA Replication Ability

COVID-19 has become a global pandemic caused by the SARS-CoV-2 coronavirus. SARS-CoV-2 shares many similarities with SARS coronavirus (SARS-CoV). A viral replication complex containing non-structural proteins (nsps) is the toolbox for RNA replication and transcription of both coronaviruses. In both cases, the RNA-dependent RNA polymerase (RdRp) domain of the coronaviral replication complex dictates the primary polymerase activity by cooperating with cofactors. The higher transmissibility and mortality due to SARS-CoV-2 are related to its higher RNA replication activity compared to SARS-CoV. The discrepancy between the RNA replication efficiency of SARS-CoV and SARS-CoV-2 can be understood by exploring interactions within their viral replication complexes. Our modeling of molecular interactions within the viral replication complexes of SARS-CoV and SARS-CoV-2 using molecular dynamics simulations suggests that in contrast to SARS-CoVnsp12, SARS-CoV2nsp12 prefers helices as the dominant interacting secondary motifs. The relative differences in nonbonded interactions between nsps could suggest viral RNA replication ability in coronaviruses.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11837-021-04662-6.

Interactions in Model Ionic Dyads and Triads Containing Tetrel Atoms

The interactions in model ionic YTX₃···Z (Y = NC, F, Cl, Br; X = F, Cl, Br, Z = F^-, Cl^-, Br^-, Li⁺) dyads containing the tetrel atoms, T = C, Si, Ge, were studied using ab initio computational methods, including an energy decomposition analysis, which found that the YTX₃ molecules were stabilized by both anions (via tetrel bonding) and cations (via polarization). For the tetrel-bonded dyads, both the electrostatic and polarization forces make comparable contributions to the binding in the C-containing dyads, whereas, electrostatic forces are by far the largest contributor to the binding in the Si- and Ge-containing analogues. Model metastable Li⁺···NCTCl₃···F^- (T = C, Si, Ge) triads were found to be lower in energy than the combined energy of the Li⁺ + NCTCl₃ + F^- fragments. The pair energies and cooperative energies for these highly polar triads were also computed and discussed.

Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains

The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π - π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π - π stacking interactions on the biological behavior of DNA through the description of these intermolecular forces in CpG island-like (GC-rich) chains. Furthermore, we made some comparisons with TATA box-like (TA-rich) chains in order to describe hydrogen bond and π - π stacking interactions as a function of the DNA sequence. For hydrogen bonds, we found that there is not a significant effect related to the number of base pairs. Whereas for π - π stacking interactions, the energy tended to decrease as the number of base pairs increased. We observed anticooperative effects for both hydrogen bonds and π - π stacking interactions. These results are in contrast with those of TATA box-like chains since cooperative and additive effects were found for both hydrogen bonds and π - π stacking, respectively. Based on the chemical hardness and density of states, we can conclude that proteins may interact easier with GC-rich chains. We conclude that regardless of the chain length, a protein could interact more easily with these genomics regions because the π - π stacking energies did not increase as a function of the number of base pairs, making, for the first time, a first approximation of the influence of noncovalent interaction on DNA behavior. We did all this work by means of DFT framework included in the DMol³ code (M06-L/DNP). Graphical Abstract Cartoon representation of how nocovalent interactions affect the interaction of DNA with a protein, i.e., how hydrogen bond and π - π stacking interactions influence the biological behavior of DNA.

The challenge of non-covalent interactions: theory meets experiment for reconciling accuracy and interpretation

In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model systems. Despite the fact that non-covalent interactions play a key role in several biological and technological processes, their characterization and interpretation are still far from being satisfactory. In this connection, integrated experimental and computational investigations can play an invaluable role. Indeed, a number of different issues relevant to unraveling the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. Focusing on the interaction of biological model systems with solvent molecules (e.g., water), since the hydration of the biomolecules controls their structure and mechanism of action, the study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from gas phase to solution. Although hydrogen bonding is probably the most widespread interaction in nature, other emerging classes, such as halogen, chalcogen and pnicogen interactions, have attracted much attention because of the role they play in different fields. Their understanding requires, first of all, the characterization of the directionality, strength, and nature of such interactions as well as a comprehensive analysis of their competition with other non-covalent bonds. In this review, it is shown how state-of-the-art quantum-chemical computations combined with rotational spectroscopy allow for fully characterizing intermolecular interactions taking place in molecular complexes from both structural and energetic points of view. The transition from bi-molecular complex to microsolvation and then to condensed phase is shortly addressed.

Modified Density Functional Dispersion Correction for Inorganic Layered MFX Compounds (M = Ca, Sr, Ba, Pb and X = Cl, Br, I)

MFX (M = Ca, Ba, Sr, Pb and X = Cl, Br, I) compounds have received considerable attention due to their technological application as X-ray detectors, pressure sensors, and optical data storage materials, when doped with rare-earth ions. MFX compounds belong to the class of layered materials with a tetragonal Matlockite crystal structure, characterized by weakly stacked double-halide layers along the crystallographic c-axis. These layers predominantly determine phase transitions, elastic, and mechanical properties. However, the correct description of the lattice parameter c is a challenge for most standard DFT functionals, which tend to overestimate the lattice parameter c. Because of the weak interactions between the halide layers, dispersion-corrected functionals seem to be a better choice. We investigated 11 different inorganic layered MFX compounds for which experimental data are available, with standard and dispersion-corrected functionals to assess their performance in reproducing the lattice parameter c, structural, and vibrational properties of the MFX compounds. Our results revealed that these functionals do not describe the weak interactions between the halide layers in a balanced way. Therefore, we modified Grimme's popular DFT-D2 dispersion correction scheme in two different ways by (i) replacing the dispersion coefficients and van der Waals radii with those of noble gas atoms or (ii) increasing the van der Waals radii of the MFX atoms up to 40%. Comparison with the available experimental data revealed that the latter approach applied to the PBE (Perdew-Burke-Ernzerhof)-D2 functional with 30% increased van der Waals radii, which we coined PBE-D2* (S_rvdw 1.30) is best suited to fine-tune the description of the weak interlayer interactions in MFX compounds, thus significantly improving the description of their structural, vibrational, and mechanical properties. Work is in progress applying this new, computationally inexpensive scheme to other inorganic layered compounds and periodic systems with weakly stacked layers.