σ-Hole interactions in small-molecule compounds containing divalent sulfur groups R 1—S—R 2

2020 ◽  
Vol 76 (4) ◽  
pp. 707-718
Author(s):  
Albert S. Lundemba ◽  
Dikima D. Bibelayi ◽  
Peter A. Wood ◽  
Juliette Pradon ◽  
Zéphyrin G. Yav
Keyword(s):  
Small Molecule ◽  
Crystal Engineering ◽  
Noncovalent Interactions ◽  
Interaction Strength ◽  
Lone Pair ◽  
Structural Data ◽  
Data Bank ◽  
Nbo Analysis ◽  
Model Systems ◽  
Divalent Sulfur

Hydrogen bonds, aromatic stacking contacts and σ-hole interactions are all noncovalent interactions commonly observed in biological systems. Structural data derived from the Protein Data Bank showed that methionine residues can interact with oxygen atoms through directional S...O contacts in the protein core. In the present work, the Cambridge Structural Database (CSD) was used in conjunction with ab initio calculations to explore the σ-hole interaction properties of small-molecule compounds containing divalent sulfur. CSD surveys showed that 7095 structures contained R 1—S—R 2 groups that interact with electronegative atoms like N, O, S and Cl. Frequencies of occurrence and geometries of the interaction were dependent on the nature of R 1 and R 2, and the hybridization of carbon atoms in C,C—S, and C,S—S fragments. The most common interactions in terms of frequency of occurrence were C,C—S...O, C,C—S...N and C,C—S...S with predominance of Csp 2. The strength of the chalcogen interaction increased when enhancing the electron-withdrawing character of the substituents. The most positive electrostatic potentials (V S,max; illustrating positive σ-holes) calculated on R 1—S—R 2 groups were located on the S atom, in the S—R 1 and S—R 2 extensions, and increased with electron-withdrawing R 1 and R 2 substituents like the interaction strength did. As with geometric data derived from the CSD, interaction geometries calculated for some model systems and representative CSD compounds suggested that the interactions were directed in the extensions of S—R 1 and S—R 2 bonds. The values of complexation energies supported attractive interactions between σ-hole bond donors and acceptors, enhanced by dispersion. The interactions of R 1—S—R 2 with large V S,max and nucleophiles with large negative V S,min coherently provided more negative energies. According to NBO analysis, chalcogen interactions consisted of charge transfer from a nucleophile lone pair to an S—R 1 or S—R 2 antibonding orbital. The directional σ-hole interactions at R 1—S—R 2 can be useful in crystal engineering and the area of supramolecular biochemistry.

scholarly journals Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult?

IUCrJ ◽  
2019 ◽  
Vol 6 (5) ◽  
pp. 788-793 ◽  
Author(s):  
Alice Brink ◽  
John R. Helliwell
Keyword(s):  
Small Molecules ◽  
Small Molecule ◽  
Design Research ◽  
Structural Data ◽  
Data Bank ◽  
Combine Data ◽  
Chemical Crystallography ◽  
File Formats ◽  
Structural Database ◽  
Circuitous Route

The interoperability of chemical and biological crystallographic data is a key challenge to research and its application to pharmaceutical design. Research attempting to combine data from the two disciplines, small-molecule or chemical crystallography (CX) and macromolecular crystallography (MX), will face unique challenges including variations in terminology, software development, file format and databases which differ significantly from CX to MX. This perspective overview spans the two disciplines and originated from the investigation of protein binding to model radiopharmaceuticals. The opportunities of interlinked research while utilizing the two databases of the CSD (Cambridge Structural Database) and the PDB (Protein Data Bank) will be highlighted. The advantages of software that can handle multiple file formats and the circuitous route to convert organometallic small-molecule structural data for use in protein refinement software will be discussed. In addition some pointers to avoid being shipwrecked will be shared, such as the care which must be taken when interpreting data precision involving small molecules versus proteins.

scholarly journals On the Importance of σ–Hole Interactions in Crystal Structures

Crystals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1205
Author(s):  
Antonio Frontera ◽  
Antonio Bauzá
Keyword(s):  
Lewis Acids ◽  
Noncovalent Interactions ◽  
Noble Gas ◽  
Lone Pair ◽  
Halogen Bonding ◽  
Lewis Base ◽  
Model Systems ◽  
Aromatic Rings ◽  
Potential Surfaces ◽  
Dual Character

Elements from groups 14–18 and periods 3–6 commonly behave as Lewis acids, which are involved in directional noncovalent interactions (NCI) with electron-rich species (lone pair donors), π systems (aromatic rings, triple and double bonds) as well as nonnucleophilic anions (BF4−, PF6−, ClO4−, etc.). Moreover, elements of groups 15 to 17 are also able to act as Lewis bases (from one to three available lone pairs, respectively), thus presenting a dual character. These emerging NCIs where the main group element behaves as Lewis base, belong to the σ–hole family of interactions. Particularly (i) tetrel bonding for elements belonging to group 14, (ii) pnictogen bonding for group 15, (iii) chalcogen bonding for group 16, (iv) halogen bonding for group 17, and (v) noble gas bondings for group 18. In general, σ–hole interactions exhibit different features when moving along the same group (offering larger and more positive σ–holes) or the same row (presenting a different number of available σ–holes and directionality) of the periodic table. This is illustrated in this review by using several examples retrieved from the Cambridge Structural Database (CSD), especially focused on σ–hole interactions, complemented with molecular electrostatic potential surfaces of model systems.

scholarly journals Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases

2020 ◽  
Vol 21 (4) ◽  
pp. 1352 ◽  
Author(s):  
János András Mótyán ◽  
Márió Miczi ◽  
József Tőzsér
Keyword(s):  
Structural Characteristics ◽  
Limited Proteolysis ◽  
Structural Data ◽  
Data Bank ◽  
Life Cycles ◽  
Evolutionary Relationships ◽  
Multiple Sequence ◽  
Dimer Interface ◽  
Viral Proteases ◽  
Eukaryotic Organisms

The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.

Structure, stability and folding of the α-helix

2001 ◽  
Vol 68 ◽  
pp. 95-110 ◽  
Author(s):  
Andrew J. Doig ◽  
Charles D. Andrew ◽  
Duncan A. E. Cochran ◽  
Eleri Hughes ◽  
Simon Penel ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrophobic Interactions ◽  
Data Bank ◽  
Site Directed Mutagenesis ◽  
Model Systems ◽  
Side Chain ◽  
Structure Stability ◽  
Helical Peptides ◽  
Vast Number ◽  
Α Helix

Pauling first described the α-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 310-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or αL C-cap motif. The kinetics of α-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

On the propagation of errors

2013 ◽  
Vol 69 (10) ◽  
pp. 1865-1866 ◽  
Author(s):  
Mariusz Jaskolski
Keyword(s):  
Protein Data Bank ◽  
Small Molecule ◽  
Data Bank ◽  
Propagation Of Errors ◽  
Small Molecule Ligand

The policy of the Protein Data Bank (PDB) that the first deposition of a small-molecule ligand, even with erroneous atom numbering, sets a precedent over accepted nomenclature rules is disputed. Recommendations regarding ligand molecules in the PDB are suggested.

scholarly journals The influence of stereochemically active lone-pair electrons on crystal symmetry and twist angles in lead apatite-2Htype structures

2014 ◽  
Vol 78 (2) ◽  
pp. 325-345 ◽  
Author(s):  
T. Baikie ◽  
M. Schreyer ◽  
F. Wei ◽  
J. S. Herrin ◽  
C. Ferraris ◽  
...  
Keyword(s):  
Single Crystal ◽  
Twist Angle ◽  
Lone Pair ◽  
Structural Data ◽  
Structural Adaptation ◽  
X Ray Diffraction ◽  
Temperature Changes ◽  
Waste Stabilization ◽  
Lone Pair Electrons ◽  
Oxide Ion

AbstractLead-containing (Pb-B-X)-2Hapatites encompass a number of [AF]4[AT]6[(BO4)6]X2compounds used for waste stabilization, environmental catalysis and ion conduction, but the influence of the stereochemically active lone-pair electrons of Pb2+on crystal chemistry and functionality is poorly understood. This article presents a compilation of existing structural data for Pb apatites that demonstrate paired electrons of Pb2+at both theAFandATresults in substantial adjustments to the PbFO6metaprism twist angle, φ. New structure refinements are presented for several natural varieties as a function of temperature by single-crystal X-ray diffraction (XRD) of vanadinite-2H(ideally Pb10(VO4)6Cl2), pyromorphite-2H(Pb10(PO4)6Cl2), mimetite-2H/M(Pb10(As5+O4)6Cl2) and finnemanite-2H(Pb10(As3+O3)6Cl2). A supercell for mimetite is confirmed using synchrotron single-crystal XRD. It is suggested the superstructure is necessary to accommodate displacement of the stereochemically active 6s2lone-pair electrons on the Pb2+that occupy a volume similar to an O2−anion. We propose that depending on the temperature and concentration of minor substitutional ions, the mimetite superstructure is a structural adaptation common to all Pb-containing apatites and by extension apatite electrolytes, where oxide ion interstitials are found at similar positions to the lonepair electrons. It is also shown that plumbous apatite framework flexes substantially through adjustments of the PbFO6metaprism twist-angles (φ) as the temperature changes. Finally, crystalchemical [100] zoning observed at submicron scales will probably impact on the treatment of diffraction data and may account for certain inconsistencies in reported structures.

Analyzing Motion Properties of Proteins Affected by Localized Structures From a Robot Kinematics Perspective

2015 ◽  
Author(s):  
Keisuke Arikawa
Keyword(s):  
Protein Data Bank ◽  
Complex Shape ◽  
Structural Data ◽  
Data Bank ◽  
Robot Kinematics ◽  
Motion Prediction ◽  
Serial Manipulators ◽  
Localized Structures ◽  
Motion Modes ◽  
Structural Compliance

On the basis of robot kinematics, we have thus far developed a method for predicting the motion of proteins from their 3D structural data given in the Protein Data Bank (PDB data). In this method, proteins are modeled as serial manipulators constrained by springs and the structural compliance properties of the models are evaluated. We focus on localized instead of whole structures of proteins. Employing the same model used in our method of motion prediction, the motion properties of the localized structures and the relation between the motion properties of localized and whole structures are analyzed. First, we present a method for graphically expressing the deformation of objects with a complex shape, such as proteins, by approximating the shape as a rectangular prism with a mesh on its surface. We then formulate a method for comparing the motion properties of localized structures cleaved from the whole structure and those remaining in it by expressing the motion of the latter using the decomposed motion modes of the former according to the structural compliance. Finally, we show a method for evaluating the effect of a localized structure on the motion properties of proteins by applying forces to localized structures. In the formulations, we demonstrate applications as illustrative examples using the PDB data of a real protein.

scholarly journals Unsaturated and Benzannulated N-Heterocyclic Carbene Complexes of Titanium and Hafnium: Impact on Catalysts Structure and Performance in Copolymerization of Cyclohexene Oxide with CO2

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4364
Author(s):  
Lakshmi Suresh ◽  
Ralte Lalrempuia ◽  
Jonas B. Ekeli ◽  
Francis Gillis-D’Hamers ◽  
Karl W. Törnroos ◽  
...  
Keyword(s):  
Density Functional ◽  
Lone Pair ◽  
Catalytic Performance ◽  
Nbo Analysis ◽  
Cyclohexene Oxide ◽  
Group 4 ◽  
Low Co2 ◽  
And Performance ◽  
High Yields ◽  
Oxygen Lone Pair

Tridentate, bis-phenolate N-heterocyclic carbenes (NHCs) are among the ligands giving the most selective and active group 4-based catalysts for the copolymerization of cyclohexene oxide (CHO) with CO2. In particular, ligands based on imidazolidin-2-ylidene (saturated NHC) moieties have given catalysts which exclusively form polycarbonate in moderate-to-high yields even under low CO2 pressure and at low copolymerization temperatures. Here, to evaluate the influence of the NHC moiety on the molecular structure of the catalyst and its performance in copolymerization, we extend this chemistry by synthesizing and characterizing titanium complexes bearing tridentate bis-phenolate imidazol-2-ylidene (unsaturated NHC) and benzimidazol-2-ylidene (benzannulated NHC) ligands. The electronic properties of the ligands and the nature of their bonds to titanium are studied using density functional theory (DFT) and natural bond orbital (NBO) analysis. The metal–NHC bond distances and bond strengths are governed by ligand-to-metal σ- and π-donation, whereas back-donation directly from the metal to the NHC ligand seems to be less important. The NHC π-acceptor orbitals are still involved in bonding, as they interact with THF and isopropoxide oxygen lone-pair donor orbitals. The new complexes are, when combined with [PPN]Cl co-catalyst, selective in polycarbonate formation. The highest activity, albeit lower than that of the previously reported Ti catalysts based on saturated NHC, was obtained with the benzannulated NHC-Ti catalyst. Attempts to synthesize unsaturated and benzannulated NHC analogues based on Hf invariably led, as in earlier work with Zr, to a mixture of products that include zwitterionic and homoleptic complexes. However, the benzannulated NHC-Hf complexes were obtained as the major products, allowing for isolation. Although these complexes selectively form polycarbonate, their catalytic performance is inferior to that of analogues based on saturated NHC.

scholarly journals Noble Gas Bonding Interactions Involving Xenon Oxides and Fluorides

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3419 ◽  
Author(s):  
Antonio Frontera
Keyword(s):  
Crystal Engineering ◽  
Lewis Acids ◽  
Noncovalent Interactions ◽  
Noble Gas ◽  
Physical Nature ◽  
Short Review ◽  
Experimental Investigations ◽  
Inorganic Crystal Structure Database ◽  
Systematic Nomenclature ◽  
Structural Database

Noble gas (or aerogen) bond (NgB) can be outlined as the attractive interaction between an electron-rich atom or group of atoms and any element of Group-18 acting as an electron acceptor. The IUPAC already recommended systematic nomenclature for the interactions of groups 17 and 16 (halogen and chalcogen bonds, respectively). Investigations dealing with noncovalent interactions involving main group elements (acting as Lewis acids) have rapidly grown in recent years. They are becoming acting players in essential fields such as crystal engineering, supramolecular chemistry, and catalysis. For obvious reasons, the works devoted to the study of noncovalent Ng-bonding interactions are significantly less abundant than halogen, chalcogen, pnictogen, and tetrel bonding. Nevertheless, in this short review, relevant theoretical and experimental investigations on noncovalent interactions involving Xenon are emphasized. Several theoretical works have described the physical nature of NgB and their interplay with other noncovalent interactions, which are discussed herein. Moreover, exploring the Cambridge Structural Database (CSD) and Inorganic Crystal Structure Database (ICSD), it is demonstrated that NgB interactions are crucial in governing the X-ray packing of xenon derivatives. Concretely, special attention is given to xenon fluorides and xenon oxides, since they exhibit a strong tendency to establish NgBs.

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