Substituent effects on CL···N, S···N, and P···N noncovalent bonds

Cl, S, and P atoms have previously been shown as capable of engaging in a noncovalent bond with the N atom on another molecule. The effects of substituents B on the former atoms on the strength of this bond are examined, and it is found that the binding energy climbs in the order B = CH(3) < NH(2) < CF(3) < OH < Cl < NO(2) < F. However, there is some variability in this pattern, particularly for the NO(2) group. The A···N bonds (A = Cl, S, P) can be quite strong, amounting to as much as 10 kcal/mol. The binding energy arises from approximately equal contributions from its induction and electrostatic components, although the former becomes more dominant for the stronger bonds. The induction energy is due in large measure to the transfer of charge from the N lone pair to a B-A σ* antibonding orbital of the electron-acceptor molecule containing Cl, S, or P. These A···N bonds typically represent the lowest-energy structure on each potential energy surface, stronger than H-bonds such as NH···F, CH···N, or SH···N.     

Effects of substituents upon the P···N noncovalent interaction: the limits of its strength

Previous work has documented the ability of the P atom to form a direct attractive noncovalent interaction with a N atom, based in large measure on the charge transfer from the N lone pair into the σ* antibonding orbital of the P-H that is turned away from the N atom. As the systems studied to date include only hydrides, the present work considers how substituents affect the interaction and examines whether P···N might compete with other attractive forces such as H-bonds. It is found that the addition of electron-withdrawing substituents greatly strengthens the P···N interaction to the point where it exceeds that of the majority of H-bonds. The highest interaction energy occurs in the FH(2)P···N(CH(3))(3) complex, amounting to 11 kcal/mol. A breakdown of the individual forces involved attributes the stability of the interaction to approximately equal parts electrostatic and induction energy, with a smaller contribution from dispersion.     

Structural organization and dimensionality at the hands of weak intermolecular Au···Au, Au···X and X···X (X = Cl, Br, I) interactions

The salts K[AuCl(2)(CN)(2)]·H(2)O (1), K[AuBr(2)(CN)(2)]·2H(2)O (2) and K[AuI(2)(CN)(2)]·?H(2)O (3) were synthesized and structurally characterized. Compound 1 crystallizes as a network of square planar [AuCl(2)(CN)(2)](-) anions separated by K(+) cations. However, 2 and 3 feature 2-D sheets built by the aggregation of [AuX(2)(CN)(2)](-) anions via weak, intermolecular X···X interactions. The mixed anion double salts K(3)[Au(CN)(2)](2)[AuBr(2)(CN)(2)]·H(2)O (4) and K(5)[Au(CN)(2)](4)[AuI(2)(CN)(2)]·2H(2)O (5) were also synthesized by cocrystallization of K[Au(CN)(2)] and the respective K[AuX(2)(CN)(2)] salts. Similarly to 2 and 3, the [Au(CN)(2)](-) and [AuX(2)(CN)(2)](-) anions form 2-D sheets via weak, intermolecular Au(I)···X and Au(I)···Au(I) interactions. In the case of 5, a rare unsupported Au(I)···Au(III) interaction of 3.5796(5) ? is also seen between the two anionic units. Despite the presence of Au(I) aurophilic interactions of 3.24-3.45 ?, neither 4 nor 5 exhibit any detectable emission at room temperature, suggesting that the presence of Au(I)···X or Au(I)···Au(III) interactions may affect the emissive properties.     

Investigation of the noncovalent interactions between anti-amyloid agents and amyloid β peptides by ESI-MS

This paper describes an efficient and reproducible screening method for identifying low molecular weight compounds that bind to amyloid β peptides (Aβ) peptides using electrospray ionization mass spectrometry (ESI-MS). Low molecular weight compounds capable of interacting with soluble Aβ may be able to modulate/inhibit the Aβ aggregation process and serve as potential disease-modifying agents for AD. The present approach was used to rank the binding affinity of a library of compounds to Aβ1-40 peptide. The results obtained show that low molecular weight compounds bind similarly to Aβ1-42, Aβ1-40, as well as Aβ1-28 peptides and they underline the critical role of Aβ peptide charge motif in binding at physiological pH. Finally, some elements of structure-activity relationship (SAR) involved in the binding affinity of homotaurine to soluble Aβ peptides are discussed.     

Dynamics of noncovalent interactions in all-α and all-β class proteins: implications for the stability of amyloid aggregates

A fully folded functional protein is stabilized by several noncovalent interactions. When a protein undergoes conformational motions, the existing noncovalent interactions may be maintained. They may also break or new interactions may be formed. Knowledge of the dynamical nature of the different types of noncovalent interactions is extremely important to understand the structural stability, function, and folding of a protein. There are experimental limitations to investigate the dynamics of different noncovalent interactions simultaneously in a biomolecule. We have carried out molecular dynamics simulations on four different proteins, two belonging to all-α class proteins and the other two are representatives of all-β class proteins. The dynamical nature of eight different noncovalent interactions was studied by monitoring the maximum residence time (MRT) and lifetime (LT). The conventional hydrogen bonds are the dominant interactions in all four proteins, and the majority of those formed between the main-chain atoms were maintained during most of the simulation time with MRT greater than 10 ns. Such interactions with more than 1 ns lifetime provide stability to the secondary structures, and hence they are responsible for the overall stability of the protein. The weak C-H···O hydrogen bond is the next major type of interactions. However, a large number of such interactions are observed between the main-chain atoms only in all-β proteins as interstrand interactions, and, surprisingly, they are observed during most part of the simulation although their average lifetime is only about 20 to 30 ps. The strong cation···π and salt-bridge interactions are present few in number. However, in many cases they are almost uninterrupted indicating the higher strength of these interactions. Four other interactions involving the π-electron cloud of aromatic rings are very small in number, and, in many cases, their presence is not maintained throughout the simulation. Our results clearly indicate that the weak C-H···O interactions between the main-chain atoms are the distinguishing factor between the all-α and all-β class of proteins, and these interstrand interactions can provide additional stability to all-β protein structures. Based on these results, we hypothesize that such weak C-H···O interstrand interactions could play a major role in providing stability to amyloid type of aggregates that are responsible for the pathological state of many proteins.     

On the directionality of anion-π interactions

The directionality of two important noncovalent interactions involving aromatic rings (namely anion-π and cation-π) is investigated. It has been recently published that the anion-π interactions observed in X-ray structures where the anion is located exactly over the center of the ring are scarce compared to cation-π interactions. To explain this behavior, we have analyzed how the interaction energy (RI-MP2/aug-cc-pVDZ level of theory) is affected by moving the anion from the center of the ring to several directions in anion-π complexes of chloride with either hexafluorobenzene or trifluoro-s-triazine. We have compared the results with the directionality of the cation-π interaction in the sodium-benzene complex. The results are useful to explain the experimental differences between both ion-π interactions. We have also computed the van der Waals radii of several halide anions and we have compared them to the neutral halogen atoms.     

Intermolecular interactions and electrostatic properties of the β-hydroquinone apohost: implications for supramolecular chemistry

The crystal structure of the β-polymorph of hydroquinone (β-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated with the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/?(2) (0.27 V/?) 1 ? along the 3-fold axis and 0.0105 e/?(2) (0.15 V/?) 1 ? along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.     

Nature and strength of C-H···O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H···O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of α-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H···O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H···O interactions in the crystal packing of formyl compounds.     

Role of saturability of noncovalent interactions in the analysis of the three-dimensional structure—opioid activity relationship

The effect of the saturability of noncovalent interactions on the character of opioid activity of opioid receptor ligands belonging to different structural classes was investigated. A three-dimensional model for an opiate pharmacophore was used to show that the involvement of pharmacophore elements, which are responsible for the agonist ligand binding to opioid receptors, in intramolecular interactions gives rise to antagonistic properties.     

Importance of halogen···halogen contacts for the structural and magnetic properties of CuX2(pyrazine-N,N′-dioxide)(H2O)2 (X = Cl and Br)

The structural and magnetic properties of the newly crystallized CuX(2)(pyzO)(H(2)O)(2) (X = Cl, Br; pyzO = pyrazine-N,N'-dioxide) coordination polymers are reported. These isostructural compounds crystallize in the monoclinic space group C2/c with, at 150 K, a = 17.0515(7) ?, b = 5.5560(2) ?, c = 10.4254(5) ?, β = 115.400(2)°, and V = 892.21(7) ?(3) for X = Cl and a = 17.3457(8) ?, b = 5.6766(3) ?, c = 10.6979(5) ?, β = 115.593(2)°, and V = 950.01(8) ?(3) for X = Br. Their crystal structure is characterized by one-dimensional chains of Cu(2+) ions linked through bidentate pyzO ligands. These chains are joined together through OH···O hydrogen bonds between the water ligands and pyzO oxygen atoms and Cu-X···X-Cu contacts. Bulk magnetic susceptibility measurements at ambient pressure show a broad maximum at 7 (Cl) and 28 K (Br) that is indicative of short-range magnetic correlations. The dominant spin exchange is the Cu-X···X-Cu supersuperexchange because the magnetic orbital of the Cu(2+) ion is contained in the CuX(2)(H(2)O)(2) plane and the X···X contact distances are short. The magnetic data were fitted to a Heisenberg 1D uniform antiferromagnetic chain model with J(1D)/k(B) = -11.1(1) (Cl) and -45.9(1) K (Br). Magnetization saturates at fields of 16.1(3) (Cl) and 66.7(5) T (Br), from which J(1D) is determined to be -11.5(2) (Cl) and -46.4(5) K (Br). For the Br analog the pressure dependence of the magnetic susceptibility indicates a gradual increase in the magnitude of J(1D)/k(B) up to -51.2 K at 0.84 GPa, suggesting a shortening of the Br···Br contact distance under pressure. At higher pressure X-ray powder diffraction data indicates a structural phase transition at ～3.5 GPa. Muon-spin relaxation measurements indicate that CuCl(2)(pyzO)(H(2)O)(2) is magnetically ordered with T(N) = 1.06(1) K, while the signature for long-range magnetic order in CuBr(2)(pyzO)(H(2)O)(2) was much less definitive down to 0.26 K. The results for the CuX(2)(pyzO)(H(2)O)(2) complexes are compared to the related CuX(2)(pyrazine) materials.     

A new noncovalent force: comparison of P···N interaction with hydrogen and halogen bonds

When PH(3) is paired with NH(3), the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom. Quantum calculations indicate that this attraction is due in part to the transfer of electron density from the lone pair of the N atom to the σ(?) antibond of a P-H covalent bond. Unlike a H-bond, the pertinent hydrogen is oriented about 180° away from, instead of toward, the N, and the N lone pair overlaps with the lobe of the P-H σ(?) orbital that is closest to the P. In contrast to halogen bonds, there is no requirement of a σ-hole of positive electrostatic potential on the P atom, nor is it necessary for the two interacting atoms to be of differing potential. In fact, the two atoms can be identical, as the global minimum of the PH(3) homodimer has the same structure, characterized by a P···P attraction. Natural bond orbital analysis, energy decomposition, and visualization of total electron density shifts reveal other similarities and differences between the three sorts of molecular interaction.     

Rapid and accurate evaluation of the binding energies and the individual N-H···O=C, N-H···N, C-H···O=C, and C-H···N interaction energies for hydrogen-bonded peptide-base complexes

The binding energies of thirty-six hydrogen-bonded peptide-base complexes, including the peptide backbone-ase complexes and amino acid side chain-base complexes, are evaluated using the analytic potential energy function established in our lab recently and compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparison indicates that the analytic potential energy function yields the binding energies for these complexes as reasonable as MP2 does, much better than the force fields do. The individual N H…O=C, N H…N, C H…O=C, and C H…N attractive interaction energies and C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interaction energies, which cannot be easily obtained from ab initio calculations, are calculated using the dipole-dipole interaction term of the analytic potential energy function. The individual N H…O=C, C H…O=C, C H…N attractive interactions are about 5.3±1.8, 1.2±0.4, and 0.8 kcal/mol, respectively, the individual N H … N could be as strong as about 8.1 kcal/mol or as weak as 1.0 kcal/mol, while the individual C=O…O=C, N H…H N, C H…H N, and C H…H C repulsive interactions are about 1.8±1.1, 1.7±0.6, 0.6±0.3, and 0.35±0.15 kcal/mol. These data are helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies.     

Synthesis of B←N embedded indacenodithiophene chromophores and effects of bromine atoms on photophysical properties and energy levels

Developing novel fused π-conjugated chromophores has been an energetic research realm and knowing how to adjust their photophysical properties and energy levels through structure tailoring is of pivotal importance. Herein, based on the ladder-type π-conjugated indacenodithiophene (IDT) moiety, four B←N embedded IDT structures, namely, BNIDT, BNIDT-2Br, BNIDT-4Br, and BNIDT-6Br are synthesized and fully characterized. The influences of B←N unit embedded in the IDT backbone and Br atoms anchoring at the periphery on the photophysical properties and energy levels are discussed systematically. From IDT to BNIDT, a new intra-molecular charge transfer (ICT) transition band appears at lower energy (400–600?nm) in the absorption spectra with reduced optical bandgaps (E_g) from 3.25?eV to 2.11?eV and the fluorescence emission peaks red-shift from 390?nm to 565?nm along with remarkably extended fluorescence lifetimes from 1.2 ns to 12.4 ns due to the introduction of electron-deficient B←N into the backbone. Further anchoring Br atoms at the periphery of the backbone gives rise to depressed optical bandgaps, decreased fluorescence quantum yields (Φ), and shortened fluorescence lifetimes (τ) from BNIDT (E_g?=?2.11?eV, Φ?=?0.46, τ?=?12.4?ns), BNIDT-2Br (E_g?=?2.08?eV, Φ?=?0.18, τ?=?4.9?ns), BNIDT-4Br (E_g?=?1.67?eV, non-emission) to BNIDT-6Br (E_g?=?1.61?eV, non-emission). The HOMO and LUMO levels estimated from ultraviolet photoelectron spectroscopy (UPS) and optical bandgaps also experience synergetic lowering from IDT to BNIDT-6Br. This work indicates that backbone modification with electron-deficient B←N unit and side groups tailoring with halogen atoms are powerful to manipulate the optical properties and energy levels of fused π-conjugated chromophores.     

Synthesis of novel O-alkylbenzochromeno-1,5-benzodiazepinones. Study of the N–H····N and CO····HN hydrogen bonding interactions with 2-aminopyridines

A series of novel 6-(O-alky)lbenzochromeno-1,5-benzodiazepin-2-ones 4a–c was prepared through the condensation between the [1]benzopyrano[4,3-c][1,5]benzodiazepin-7(8H)one 1 and a series of alkylalcohols. Scaffold 4 exhibited interesting hydrogen-bonding interaction with 2-aminopyridine derivatives. The so obtained self-assembled systems 5 were fully characterized by 1D/2D-NMR techniques and mass spectrometry. The hydrogen-bonding interaction was supported by IR and Raman spectroscopy and by ¹H NMR titration experiments, and was confirmed by an X-ray crystal structure analysis.     

Study on the influence of ageing on chemical and mechanical properties of N,N′-dimethyl-N,N′-diphenylcarbamide stabilized propellants

Double-base propellants undergo chemical, physical and mechanical changes upon ageing, leading to changes in ballistic performance and presenting explosive hazards. This report studies the variation of chemical and mechanical properties of aged N,N′-dimethyl-N,N′-diphenylcarbamide (methyl centralite) stabilized propellants in order to simulate and evaluate the natural ageing throughout the artificial one. Therefore, a comparative study of stabilizer depletion, plasticizers content, heat of combustion and mechanical properties such as storage modulus, loss modulus and damping of naturally and artificially aged propellants has been carried out by the following techniques: high-performance liquid chromatography (HPLC), thermogravimetric analyzer (TG), calorimeter of combustion and dynamic mechanical analyzer (DMA), respectively. The results obtained show that all properties are closely connected. In addition, the determination of stabilizer depletion, plasticizers evaporation, decrease of heat of combustion and mechanical properties are very useful for a better understanding of the decomposition and ageing behaviour of propellants. The HPLC investigation of stabilizer has shown good stability of the propellants. The results obtained for DMA have shown that some considerable changes of the mechanical and viscoelastic properties of the propellants occurred during ageing. These results confirm the results obtained by TG for the reduction of the nitroglycerine amount and the decrease of the heat of combustion.     

On the effect of thermophoretic force,gravitational force,and particle–particle interactions in field-flow fractionation

The theoretical calculations confirmed that the gravitational force cannot be neglected in all field-flow fractionation techniques separating nanometer-sized colloidal particles whenever particle diameter is approximately 200?nm and larger. Particle–particle repulsive interactions, mostly electrostatic repulsions, influence substantially concentration distribution established by any effective field acting across the fractionation channel, as confirmed explicitly for thermophoretic force generated by temperature gradient in microthermal field-flow fractionation. The ionic strength of the carrier liquid causes the screening of the electrostatic double layer around the dispersed particles and thus influences the retention. The attractive particle–particle forces occur when the zeta potential of the particles approaches to 0?mV, the electrostatic repulsions are screened, and the aggregation of the particles is observed. The pH influences differently the size and zeta potential of the plain polystyrene latex particles and of the particles modified on the surface by the groups –COOH and –NH₂. The role of a detergent in carrier liquid is non-negligible, as demonstrated by its presence or absence in carrier liquid.     

The effect of structure and phase transformation on the mechanical properties of Re₂N and the stability of Mn₂N

First‐principles calculations were carried out on recently synthesized Re₂ and Re₃ as well as hypothetical Tc and Mn nitrides. It is found that structure and covalent bonds play an important role in determining mechanical properties. Under a large strain along (0001)〈101 0〉direction, Re₂N undergoes a phase transformation with a slight increase in ideal shear strength. On the other hand, it is transformed into a phase with weaker mechanical properties, if the strain is along Re₂〈1 21 0〉 direction. Mn₂N can be synthesized under moderate conditions due to its more negative formation energy. Re₂N, Re₃N, and Mn₂N show structure‐related mechanical property under larger strains to ReB₂ but exhibit much lower ideal strengths, which is attributed to the larger ionicity of cation–anion bond. Three‐dimensional framework of strong covalent bonds is thus highly recommended to design superhard materials. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Can the DFT-D method describe the full range of noncovalent interactions found in large biomolecules?

The DFT-D method is shown to yield interaction energies between biologically important groups to an accuracy comparable to that obtained using state-of-the-art ab initio methods.     

Toward the exact solution of the electronic Schrödinger equation for noncovalent molecular interactions: worldwide distributed quantum monte carlo calculations

Quantum Monte Carlo (QMC) calculations on the stacked (st) and Watson/Crick (wc) bound adenine/thymine (A/T) and cytosine/guanine (C/G) DNA base pair complexes were made possible with the first large scale distributed computing project in ab initio quantum chemistry, Quantum Monte Carlo at Home (QMC@HOME). The results for the interaction energies (wc-A/T = 15.7 kcal/mol, wc-C/G = 30.2 kcal/mol, st-A/T = 13.1 kcal/mol, st-C/G = 19.6 kcal/mol) are in very good agreement with the best known coupled-cluster based estimates. The accuracy of these values is further supported by calculations on the S22 benchmark set of noncovalently bound systems, for which we obtain a small mean absolute deviation of 0.68 kcal/mol. Our results support previous claims that the stacking energies are of comparable magnitude to the interactions of the commonly discussed hydrogen-bonded motif. Furthermore, we show that QMC can serve as an advantageous alternative to conventional wave function methods for large noncovalently bound systems. We also investigated in detail all technical parameters of the QMC simulations and recommend a careful optimization procedure of the Jastrow correlation factors in order to obtain numerically stable and reliable results.     

Description of noncovalent interactions involving π-system with high precision: An assessment of RPA,MP2, and DFT-D methods

Efficient approaches with high precision are essential for understanding the formation and stability of noncovalent interaction complexes. Here, 21 noncovalent interaction complexes involving π-system are selected and grouped in three subsets according to ETS–NOCV method: dispersion-dominated, electrostatic-dominated, and mixed. We mainly focus on examining the performance of random-phase approximation (RPA) on these π systems. The tested RPA-based method includes standard RPA and its variants including the related single excitations (SEs), renormalized single excitations (rSEs), second-order screened exchange (SOSEX), and the renormalized second-order perturbation theory (rPT2). The routine second-order Møller–Plesset perturbation theory (MP2) and three popular DFT-D functionals (M06-2X-D3, ωB97XD, and PBE-D3(BJ)) are also assessed for comparison. In this work, besides the calculation of interaction energies at Dunning-type aug-cc-pVDZ and aug-cc-pVTZ basis set, we also present a larger database of interaction energies calculated using MP2 and RPA methods with Dunning-type aug-cc-pVQZ basis set. An accurate CCSD(T)/CBS scheme is used to provide benchmark database. In addition to the high-level results, we also provide potential energy surfaces (PES) of different interaction type. Among all the tested methods, MP2 has a satisfactory performance on electrostatic-dominated and mixed-type systems, except for dispersion-dominated systems. DFT-D functionals, especially ωB97XD functional, has a balanced performance across all the tested systems. Importantly, for RPA-based methods, the calculation accuracy can be dramatically improved by taking into account SE or exchange effects, especially in the mixed complexes. We conclude that rPT2 among all the test RPA-based methods gives an overall satisfactory performance across different interaction types. © 2019 Wiley Periodicals, Inc.