Analysis Of Intermolecular Contacts Research Articles

Structural Origins of the Anisotropic Thermal Expansion of BINOL Crystals

Measurement of the unit cell of (R)-BINOL over a 200° temperature range (300–100 K) reveals an anisotropic contraction where the c-axis contracts ca. 2.3% compared to a ca. 0.45% contraction of the a and b axes, a ca. six-fold difference in linear thermal expansion coefficient. This contraction corresponds to a decrease in the helical pitch of the 31 screw axis in the [001] direction. The anisotropic nature of the contraction is rationalised by a thorough analysis of intermolecular contacts within the crystal and their impact on the conformation of the molecule and crystal packing.Graphical The crystal structure of (R)-BINOL exhibits a pronounced anisotropic thermal expansion.

Ketoiminate versus diketonate ligand to improve lithium precursor properties: Structural consideration of two analogues

An approach is proposed to design new lithium MOCVD precursors by minor ligand modification. It has been shown that β-ketoiminate ligand can significantly improve the properties of volatile lithium complexes compared to β-diketonate analogues. For this purpose, the structure and properties of two volatile lithium complexes with similar bulky ligands are compared: for β-diketonate Li(tmhd) (1) (tmhd = 2,2,6,6-tetramethyl-heptane-3,5-dionate or dipivaloylmethanate, tBu-CO-CH-CO-tBu, where tBu = C(CH3)3) and β-ketoiminate Li(tmha) (2) (tmha = 2,2,6,6-tetramethyl-heptane-3-imino-5-onate, tBu-CO-CH-C(NH)-tBu). Compound 2 is new, and is formally derived from 1 by substitution of oxygen donor atom by NH-group. The compounds were prepared by the same technique and were studied by X-ray diffraction and IR and Raman spectroscopy. Molecular structure of these complexes is similar, built of tetrameric aggregates [LiL]4 with cubane-like Li4O4 core. Both 1 and 2 crystallize in C2/c space group with Z = 4 and Z’ = 0.5 but with different packing motif. According to DSC data, only 2 experiences a crystal-to-crystal phase transition at 384 K, which manifests itself as a shift of molecular rows along the a axis, while geometry of [Li(tmha)]4 and crystal space group remain unchanged. Analysis of intermolecular contacts using Hirshfeld surface analysis showed that [Li(tmha)]4 molecules are less densely packed compared to [Li(tmhd)]4. This explains the greater volatility of 2 compared to 1, due to the lower value of the lattice energy.

Evolution of intermolecular contacts with temperature and pressure in bromoethane and iodoethane – a comparative study

At ambient conditions two liquids, bromoethane, C2H5Br (MBE, m.p. 154.6 K) and iodoethane, C2H5I (MIE, m.p. 162.1 K), have been crystallized under both isobaric and isochoric conditions using in situ low-temperature and high-pressure techniques. The single-crystal X-ray diffraction studies, supported by the isothermal compressibility and isobaric differential scanning calorimetry measurements, allowed the monitoring and analysis at low temperature and high pressure of the effects of externally induced changes in MBE and MIE. The monoclinic MBE and MIE crystals are found to be isostructural. They are stable, in the investigated regimes, i.e. down to 100 K/0.1 MPa and up to ∼295 K/3.7 GPa, without undergoing any symmetry or phase change. Both the contraction and compression is mainly noted for the intermolecular separation distances. The Hirshfeld surface analysis of intermolecular contacts clearly shows the nature of occurrence and hierarchy of interactions pointing out the role played by Br/I...Br/I contacts, in particular at ambient temperature and high-pressure conditions. The preferences for the formation of intermolecular contacts in MIE are more pronounced and do not require such extreme conditions as in the case of MBE. It is notable that the Br/I...Br/I and Br/I...H contacts could be basically classified as type-I interactions.

Crystallographic, DFT, Lattice Energy and Hirshfeld Surface Analysis of Some CSD-Based 6-Chloropurines

A comparative crystallographic and detailed computational analysis of four known 6-chloropurine X-ray structures, accessed from the CSD repository, has been reported in this paper. The quantum chemical analysis of each structure, including the optimized geometry, lattice energy, Hirshfeld surface, HOMO-LUMO energies, has been made to account for the properties of this class of biologically important organic materials. The lattice energy contribution in terms of intermolecular interactions, responsible for the packing stability, has been estimated by PIXEL procedure. Three-dimensional Hirshfeld surfaces and the corresponding 2D-fingerprint plots include the analysis of short intermolecular contacts. The π…π interactions and stacking features of molecules in the packing, have been analyzed using shape index and curvedness plots.

Synthesis, X-ray structure analysis, and vibrational spectral studies of 1-(3-((6-bromopyrido[2,3-d]pyrimidin-4-yl)oxy)phenyl)- 3-cyclopentylurea

A new pyrido[2,3-d]pyrimidine derivative 1-(3-((6-bromopyrido[2,3-d]pyrimidin-4-yl)oxy)phenyl)-3-cyclopentylurea is designed and synthesized. The final structure is characterized by 1H, 13C, and 2D NMR, MS, FTIR. In addition, the crystal structure of the title compound is determined by X-ray diffraction. With the 6-311G(2d,p) basis set, the molecule is further explored using density functional theory (DFT) by the B3LYP method. The final results show that the DFT optimized structure of the title molecule is consistent with the crystal structure determined by X-ray diffraction. The Hirshfeld surface analysis and the 2D fingerprint plot are given to support the quantitative analysis of intermolecular interactions and contacts generated by supramolecular accumulation in crystals. The interactions of the title molecule are analyzed by the natural bond orbital analysis. Finally, the molecular electrostatic potential and frontier molecular orbitals are further investigated using DFT.

Synthesis, crystal structure, vibrational properties and DFT studies of 4-(furan-2-ylmethyl)-1-(thiomorpholinomethyl)-[1,2,4]triazolo[4,3-a]quinazon-5(4H)-one

In this present research, the title compound 4-(furan-2-ylmethyl)-1-(thiomorpholinomethyl)-[1,2,4]triazolo[4,3-a]quinazolin-5(4H)-one(1) was synthesized, and its single crystal was produced in acetone. The use of 1H NMR, 13C NMR, FT-IR spectroscopy and MS determined its structure. Using X-ray diffraction, the single crystal of the title compound was measured. At the same time, the optimized molecular crystal structure of this small molecule was determined according to DFT calculations adopting B3LYP/6–311 G (2d, p) basis set. The conformational isomer 1–3 is the most stable conformation and is consistent with the conformation derived from X-ray diffraction. Hirshfeld surface analysis and 2D fingerprint were given to support the quantitative analysis of intermolecular interactions and contacts caused by supramolecular accumulation in crystals.

Derivative of Scorpion Neurotoxin BeM9 Is Selective for Insect Voltage-Gated Sodium Channels

Scorpion α-toxins are small proteins inhibiting the inactivation of voltage-gated sodium channels. They can selectively act on either mammalian (mammal toxins) or insect channels (insect toxins), or affect both types of channels (α-like toxins). Currently no model has been proposed that fully explains the dependence of selectivity upon amino acid sequence, but some patterns have already been established. Thus, most mammal toxins have an aspartic acid residue in position 8, which is involved in the formation of the nest motif, but it is still not clear whether this residue interacts directly with channels. The objective of our study was to obtain a derivative of the α-like toxin BeM9 with the replacement of lysine in position 8 by glutamate (K8E), changing the charge, but excluding the formation of the nest motif. In addition, we replaced the tyrosine in position 17 with glycine (Y17G), which is characteristic of mammal toxins. Surprisingly, the double-mutant derivative BeM9EG lost its activity on mammalian channels, becoming an insect toxin. To explain these changes, we constructed models of BeM9 and BeM9EG complexes with channels, and also performed molecular dynamics of isolated toxins. Analysis of intermolecular contacts in the complexes did not explain the reason for the selectivity change. Nevertheless, the structure of intramolecular contacts and data on molecular mobility indicate an important role of residues K8 and Y17 in stabilizing a certain conformation of BeM9 loops. We assume that the replacement of these residues allosterically affects the efficiency of toxin binding to channels.

Arginine multivalency stabilizes protein/RNA condensates.

Biomolecular condensates assembled through liquid-liquid phase separation (LLPS) of proteins and RNAs are currently recognized to play an important role in cellular organization. Their assembly depends on the formation of a network of transient, multivalent interactions between flexible scaffold biomolecules. Understanding how protein and RNA sequences determine these interactions and ultimately regulate the phase separation is an open key challenge. Recent in vitro studies have revealed that arginine and lysine residues, which are enriched in most cellular condensates, have markedly distinct propensities to drive the LLPS of protein/RNA mixtures. Here, we employ explicit-solvent atomistic molecular dynamics simulations to shed light on the microscopic origin of this difference by investigating mixtures of polyU oligonucleotides with either polyR/polyK peptides. In agreement with experiments, our simulations indicate that arginine has a higher affinity for polyU than lysine both in highly diluted conditions and in concentrated solutions with a biomolecular density comparable to cellular condensate. The analysis of intermolecular contacts suggests that this differential behavior is due to the propensity of arginine side chains to simultaneously form a higher number of specific interactions with oligonucleotides, including hydrogen bonds and stacking interactions. Our results provide a molecular description of how the multivalency of the guanidinium group enables the coordination of multiple RNA groups by a single arginine residue, thus ultimately stabilizing protein/RNA condensates.

Spectroscopic Characterization, Hirshfeld Surface, DFT, and TD-DFT of tert-Butyl Phenethylcarbamate and 1,1-Dimethyl-3-Phenethylurea

Tert-butylphenethylcarbamate (1) and 1,1-dimethyl-3-phenethylurea (2) were synthesized, and their structures were confi rmed by NMR, FTIR, and mass spectrometry techniques. The experimental spectroscopic data of 1 and 2 were compared with the corresponding calculated ones obtained by density functional theory (DFT) and time-dependent DFT methods, for which the hybrid functionals B3LYP, B3P86, and PBE0 combined with the 6-311++G(d,p) basis set were tested. The solvent effect was considered using the implicit model — integral equation formalism-polarizable continuum model (IEFPCM). Relatively good correlation (R2 > 90%) was obtained between the experimental and predicted spectral data. The conformational effect on the absorption maximum λmax was negligible, that is, λmax of different conformers varied by less than 0.01 nm. Hirshfeld surface analysis and electrostatic potential calculations of the closest intermolecular contacts between active atoms of 1 and 2 revealed that the closest interactions were between hydrogen atoms of 39.6 and 46.3%, respectively.

Investigating differences and similarities between two new abiraterone polymorphs and its hydrochloride salt monohydrate

Crystal and molecular structures of two polymorphs (forms II and III) of abiraterone are presented. Both crystal modifications crystallize in the monoclinic crystal system P21 with one molecule in the asymmetric unit. Molecules are involved in strong and weak intermolecular hydrogen bonds of O-H⋅⋅⋅N and C-H⋅⋅⋅O types. Differences in crystals packing and intermolecular interactions were demonstrated by the Hirshfeld surface analysis.The spectroscopic studies showed the correlation of O⋅⋅⋅N distances with wavenumbers of OH groups for abiraterone polymorphs. The IR results agree with a density rule for form III suggesting that this form has a lower thermodynamic stability at 0 K.Abiraterone hydrochloride monohydrate is a direct product of abiraterone acetate hydrolysis under acidic conditions. The salt is unstable during crystallization and transforms into abiraterone base. The detailed description of hydrogen bonds and the analysis of main intermolecular contacts to the Hirshfeld surface of the salt measured at 100 K are presented.

Quasi-Isostructural Co(II) and Ni(II) Complexes with Mefenamato Ligand: Synthesis, Characterization, and Biological Activity.

Three metal complexes of mefenamato ligand 1 were synthesized: [Co2(mef)4(EtOH)2(H2O)4]: 2; [Co(mef)2(MeOH)4]∙2MeOH: 3; and [Ni(mef)2(MeOH)4]∙2MeOH: 4. Their compositions and properties were investigated by elemental analysis (EA), flame atomic absorption spectrometry (FAAS), Fourier-transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA). Crystal structures were determined by the single crystal X-ray diffraction technique. Additionally, their antioxidant and antimicrobial activity were established, thus proving good/moderate bioactivity against Gram-positive bacteria and yeasts. In the crystal structure of 2, an apical water molecule is shared between two adjacent cobalt(II) ions, resulting in the formation of a polymeric chain extending along the [100] direction. Meanwhile, structures 3 and 4 have strong intermolecular hydrogen bonds with diverse topologies that yield unique quasi-isostructural arrangements. The packing topology is reflected by the Hirshfeld surface analysis of intermolecular contacts.

Crystal structure, Hirshfeld surface analysis and contact enrichment ratios of 1-(2,7-di-methyl-imidazo[1,2-a]pyridin-3-yl)-2-(1,3-di-thio-lan-2-yl-idene)ethanone monohydrate.

In the title hydrated hybrid compound C14H14N2OS2·H2O, the planar imidazo[1,2-a]pyridine ring system is linked to the 1,3-di-thiol-ane moiety by an enone bridge. The atoms of the C-C bond in the 1,3-di-thiol-ane ring are disordered over two positions with occupancies of 0.579 (14) and 0.421 (14) and both disordered rings adopt a half-chair conformation. The oxygen atom of the enone bridge is involved in a weak intra-molecular C-H⋯O hydrogen bond, which generates an S(6) graph-set motif. In the crystal, the hybrid mol-ecules are associated in R 2 2(14) dimeric units by weak C-H⋯O inter-actions. O-H⋯O hydrogen bonds link the water mol-ecules, forming infinite self-assembled chains along the b-axis direction to which the dimers are connected via O-H⋯N hydrogen bonding. Analysis of inter-molecular contacts using Hirshfeld surface analysis and contact enrichment ratio descriptors indicate that hydrogen bonds induced by water mol-ecules are the main driving force in the crystal packing formation.

Intermolecular Interactions in Crystals of the Photosensitive Coordination Compounds of Zinc(II)

The distribution of the electron density function in crystals of {[ZnBpe(Me2Mal)] · H2O}n (I) and [Zn(H2O)4Bpe2](HEt2Mal)2 (II) is obtained by the periodic DFT calculations. Under UV irradiation, compounds I and II transform into [Zn(Bpe)(Me2Mal)]2[Zn2(Тpcb)(Me2Mal)2] · H2O and {[Zn(H2O)4(Bpe)2]0.15[Zn(H2O)4(Tpcb)]0.85(HEt2mMal)4} (Bpe is 1,2-bis(4-pyridine)ethylene, Тpcb is 1,2,3,4-tetrakis(4-pyridine)cyclobutane, H2Me2Mal is dimethylmalonic acid, and H2Et2Mal is diethylmalonic acid), respectively. An analysis of intermolecular contacts using Bader’s “Atoms-in-Molecules” theory shows the bonding route and bond critical point between the carbon atoms of the adjacent 1,2-bis(4-pyridine)ethylene molecules. It is established that the common surface of the Voronoi–Dirichlet molecular polyhedra between the photosensitive fragments can serve as a criterion for the possible participation of the molecules in solid-phase photoinduced reactions.

Thermally induced order–disorder transition in crystals of lithium complexes of 1,5-Bis[2-(diphenylphosphorylmethyl)phenoxy]-3-oxapenthane [LiL](ClO4) and [LiL](NCS): Effect of the anion on the temperature of transition

Compounds of 1,5-bis[2-(diphenylphosphorylmethyl)phenoxy]-3-oxapenthane (L) with lithium salts LiXL, where Х– = ClO4, NCS, or I, and LiBrL ⋅ 2H2O, are synthesized. The IR spectra and the thermal behavior of complexes are studied. X-ray diffraction studies of isostructural [LiL](ClO4) (I) and [LiL](NCS) (II) crystals are performed. In the [LiL]+ complex, the ligand coordinates the Li atom by five O atoms, forming an environment in the shape of a trigonal bipyramid [in II at 174 K, the Li–O bonds are1.829(3)–2.341(3) A]. It is found that crystals I and II undergo a reversible phase transition of the order–disorder type with the change of symmetry (P21/n ↔ P\(\bar 1\)). The temperatures of transition of crystals I and II differ by ~70°. This distinction is explained by different types of disordering of the phenyl rings of the L ligand in the monoclinic phase, namely, dynamic in I and static in II. The analysis of intermolecular contacts allows one to relate the state of disordering of ligand L in the crystal to the strength of its interactions with the anion: in II the NCS– anion is firmly fixed by the С–Н···S and С–Н···N hydrogen bonds (at 174 K, H···S is 2.77 and H···N is 2.36 A); in I the С–Н···О interactions of the ClO\(\bar 4\) anion with the ligand are weaker (at 215 K, Н···О ≥ 2.37 A) and the anion is disordered.

Interlocked aromatic species: Crystal structure and Hirshfeld surface analysis of the uranyl ion complex of 3-(pyrimidin-2-yl)benzoate with Ni(phen)32 + counter-ions

The reaction of uranyl nitrate with 3-(pyrimidin-2-yl)benzoic acid (LH) in the presence of nickel(II) nitrate and 1,10-phenanthroline (phen) yields the complex [Ni(phen)3][UO2(L)3]2·2.5H2O (1), in which the uranium atom is chelated by three carboxylate groups. Analysis of short intermolecular contacts shows that those associated with π⋯π interactions do not show up prominently, notwithstanding the number of aromatic rings present, and the packing mode appears to be primarily a result of Coulombic interactions and best shape fitting.

SNARE Protein Mimicry by an Intracellular Bacterium

Many intracellular pathogens rely on host cell membrane compartments for their survival. The strategies they have developed to subvert intracellular trafficking are often unknown, and SNARE proteins, which are essential for membrane fusion, are possible targets. The obligate intracellular bacteria Chlamydia replicate within an intracellular vacuole, termed an inclusion. A large family of bacterial proteins is inserted in the inclusion membrane, and the role of these inclusion proteins is mostly unknown. Here we identify SNARE-like motifs in the inclusion protein IncA, which are conserved among most Chlamydia species. We show that IncA can bind directly to several host SNARE proteins. A subset of SNAREs is specifically recruited to the immediate vicinity of the inclusion membrane, and their accumulation is reduced around inclusions that lack IncA, demonstrating that IncA plays a predominant role in SNARE recruitment. However, interaction with the SNARE machinery is probably not restricted to IncA as at least another inclusion protein shows similarities with SNARE motifs and can interact with SNAREs. We modelled IncA's association with host SNAREs. The analysis of intermolecular contacts showed that the IncA SNARE-like motif can make specific interactions with host SNARE motifs similar to those found in a bona fide SNARE complex. Moreover, point mutations in the central layer of IncA SNARE-like motifs resulted in the loss of binding to host SNAREs. Altogether, our data demonstrate for the first time mimicry of the SNARE motif by a bacterium.

Weak Intermolecular Interactions in the (1:1) Pyridine Solvate of Dibenzotetraaza[14]annulene Copper(II) Complex. The Crystal Structure of [7,16-dibenzoyl-6,8,15,17-tetramethyl-5,14-dihydrodibenzo[b,i][1,4,8,11] [tetraazacyclotetradecinato(2-)- k 4N]copper(II)·pyridine

Recrystallization of the title Cu(II) complex from pyridine afforded solid (1:1) pyridine inclusion compound. The crystal structure revealed a pleated-sheet-like arrangement of saddle-shaped molecules of the host, with molecules of pyridine enclathrated within intermolecular cavities. Careful analysis of intermolecular contacts showed that weak aromatic edge-to-face (C–H···Fπ) interactions occur between pyridine and host molecules. The crystal packing appeared to be also stabilized by the host–host C–H···O hydrogen bonds.

New Method of Analysis of Intermolecular Contacts in the Crystal Structure: π-Complexes

A new method for analysis of intermolecular contacts in the crystal structure based on characteristics of the Voronoi-Dirichlet polyhedra (VDP) is considered using metal π-complexes as examples. The crystal data of the compounds were used to determine the surface area of the VDP faces corresponding to all intermolecular contacts in one π-complex, the total volume of the pyramids with VDP faces as bases and the nuclei of atoms involved in the intermolecular contacts at the vertices, and the total solid angle at which the “intermolecular” VDP faces are seen from the corresponding nuclei of the molecule. A common linear correlation between the enthalpy of sublimation of π-complexes and saturated or unsaturated hydrocarbons and the molecular VDP characteristics was elucidated. On the basis of the results, the enthalpies of sublimation were calculated for some iron π-complexes (for which data on the crystal structure were available) and C60 and C70 fullerenes.

Program for analysis of intermolecular contacts in organic crystals

The ICA (Intermolecular Contacts Analysis) computer program was developed for statistical analysis of intermolecular atom-atom contacts in organic crystals. At present, the program allows one to examine homomolecular crystals belonging to monosystem structural classes. The analysis involves the following steps: selection of supporting contacts (i.e., contacts sufficient for the formation of a three-dimensional framework of intermolecular “touches”), construction of their distributions over atom-atom distances, approximation of the distribution curves by Gaussians, and calculations of the average (most probable) length of the contacts of a particular type and the variance of the distribution. The van der Waals radii of the most important organogenic elements were refined on the basis of the data on approximately 7800 crystal structures retrieved from the Cambridge Structural Database.

Electrostatic Energies in the 1,4-Dichlorobenzene Polymorph Crystals: the Role of Charge Density Overlap Effects in Crystal Packing Analysis

Electrostatic and polarization energies for the three known polymorphic crystal structures of 1,4-dichlorobenzene, as well as for one particularly stable virtual crystal structure generated by computer search, were calculated by a new accurate numerical integration method over static molecular charge densities obtained from high level ab initio molecular-orbital calculations. Results are compared with those from standard empirical atom-atom force fields. The new electrostatic energies, which include charge density overlap (penetration) effects, are seen to be much larger than and sometimes of opposite sign to those derived from point-charge models. None of the four polymorphs is substantially more stable than the others on electrostatic-energy grounds. Molecule-molecule electrostatic energies have been calculated for the more important molecular pairs in each of the four structures; trends are found to be very different from those indicated by point-charge energies or by total energies estimated with a parametric atom-atom force field. Conclusions based exclusively on analysis of intermolecular atom contacts and point-charge electrostatics may need to be modified in the light of the new kind of calculation.