The Journal of Physical Chemistry A May 11, 2017 Volume 121(Issue 18) pp:3606-3606
Publication Date(Web):April 26, 2017
DOI:10.1021/acs.jpca.7b02305
Receptors for halide anions are constructed based on the imidazolium unit and then replacing the H-bonding C–H group first by halogen-bonding C–I and then by tetrel-bonding C–SnH3 and C–SiF3. Attaching a phenyl ring to any of these species has little effect on its ability to bind a halide, but incorporation of a second imidazolium to the benzene connector, forming a bidentate dicationic receptor, greatly enhances the binding. Addition of electron-withdrawing F atoms to each imidazolium adds a further increment. F– consistently binds more strongly to the various receptor models than does Cl–. Whereas replacement of the H atom on the imidazolium groups with the halogen-bonding I has an inconsistent perturbing effect, tetrel-bonding SnH3 significantly enhances the binding with either halide, and SiF3 even more so. Placement of the various complexes into aqueous solution reduces binding energies but the trends that occur in the gas phase are largely reproduced in water. The tetrel-bonding receptors are the most selective for F– over Cl– with an equilibrium ratio on the order of 1014 for SnH3 and 1028 for SiF3. When combined with their strong halide binding, SiF3–ImF3–Bz–ImF3–SiF3+2 bipodal receptors represent an optimal choice in terms of both binding strength and selectivity.
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 7) pp:5550-5559
Publication Date(Web):2017/02/15
DOI:10.1039/C6CP07531B
Ab initio calculations have been performed for the complexes H+–PyTX3⋯NH3 and H+–furanTF3⋯NH3 (T = C, Si, and Ge; X = F and Cl) with focus on geometries, energies, orbital interactions, and electron densities to study the influence of protonation on the strength of tetrel bonding. The primary interaction mode between α/β-furanCF3/p-PyCF3 and NH3 changes from an F⋯H hydrogen bond to a C⋯N tetrel bond as a result of protonation. Importantly, the protonation has a prominent enhancing effect on the strength of tetrel bonding with an increase in binding energy from 14 to 30 kcal mol−1. The tetrel bonding becomes stronger in the order H+–p-PySiF3⋯NH3 < H+–m-PySiF3⋯NH3 < H+–o-PySiF3⋯NH3, showing a reverse trend from that of the neutral analogues. In addition, there is competition between the tetrel and hydrogen bonds in the protonated complexes, in which the hydrogen bond is favored in the complexes of H+–p-PyCF3 but the tetrel bond is preferred in the complexes of H+–p-PyTX3 (T = Si, Ge; X = F, Cl) and H+–o/m-PySiF3.
A series of halide receptors are constructed and the geometries and energetics of their binding to F−, Cl−, and Br− assessed by quantum calculations. The dicationic receptors are based on a pair of imidazolium units, connected via a benzene spacer. The imidazoliums each donate a proton to a halide in a pair of H-bonds. Replacement of the two bonding protons by Br leads to binding via a pair of halogen bonds. Likewise, chalcogen, pnicogen, and tetrel bonds occur when the protons are replaced, respectively, by Se, As, and Ge. Regardless of the binding group considered, F− is bound much more strongly than are Cl− and Br−. With respect to the latter two halides, the binding energy is not very sensitive to the nature of the binding atom, whether H or some other atom. But there is a great deal of differentiation with respect to F−, where the order varies as tetrel > H ∼ pnicogen > halogen > chalcogen. The replacement of the various binding atoms by their analogues in the next row of the periodic table enhances the fluoride binding energy by 22–56%. The strongest fluoride binding agents utilize the tetrel bonds of the Sn atom, whereas it is I-halogen bonds that are preferred for Cl− and Br−. After incorporation of thermal and entropic effects, the halogen, chalcogen, and pnicogen bonding receptors do not represent much of an improvement over H-bonds with regard to this selectivity for F−, even I which binds quite strongly. In stark contrast, the tetrel-bonding derivatives, both Ge and Sn, show by far the greatest selectivity for F− over the other halides, as much as 1013, an enhancement of six orders of magnitude when compared to the H-bonding receptor.
Co-reporter:Vincent de Paul N. Nziko and Steve Scheiner
Physical Chemistry Chemical Physics 2016 vol. 18(Issue 5) pp:3581-3590
Publication Date(Web):05 Jan 2016
DOI:10.1039/C5CP07545A
In addition to the standard halogen bond formed when NH3 approaches XCN (X = F, Cl, Br, I) along its molecular axis, a perpendicular approach is also possible, toward a π-hole that is present above the X–C bond. MP2/aug-cc-pVDZ calculations indicate the latter geometry is favored for X = F, and the σ-hole structure is preferred for the heavier halogens. The π-hole structure is stabilized by charge transfer from the NH3 lone pair into the π*(CN) antibonding orbital, and is characterized by a bond path from the N of NH3 to the C atom of XCN, a form of tetrel bond. The most stable 2:1 NH3/XCN heterotrimer for X = F and Cl is cyclic and contains a tetrel bond augmented by a pair of NH⋯N H-bonds. For X = Br and I, the favored trimer is noncyclic, stabilized by a tetrel and a halogen bond.
Physical Chemistry Chemical Physics 2016 vol. 18(Issue 27) pp:18015-18023
Publication Date(Web):13 Jun 2016
DOI:10.1039/C6CP03771B
Quantum calculations examine how the NH⋯Y H-bond compares to the equivalent NX⋯Y halogen bond, as well as to comparable CH/CX donors. Succinimide and saccharin, and their corresponding halogen-substituted derivatives, are chosen as the prototype NH/NX donors, paired with a wide range of electron donor molecules. The NH⋯Y H-bond is weakened if the bridging H is replaced by Cl, and strengthened by I; a Br halogen bond is roughly comparable to a H-bond. The lone pairs of the partner molecule are stronger electron donors than are π-systems. Whereas Coulombic forces represent the largest fraction of the attractive force in the H-bonds, induction energy is magnified in the halogen bonds, surpassing electrostatics in several cases. Mutation of NH/NX to CH/CX weakens the binding energy to roughly half its original value, while also lengthening the intermolecular distances by 0.3–0.8 Å.
Co-reporter:Okuma Emile Kasende, Aristote Matondo, Jules Tshishimbi Muya, Steve Scheiner
Computational and Theoretical Chemistry 2016 Volume 1075() pp:82-86
Publication Date(Web):1 January 2016
DOI:10.1016/j.comptc.2015.11.017
•Temozolomide (TMZ) is an important pharmaceutical.•There is little known about its interactions with other molecules.•The O atom of the terminal amide group is shown to be the preferred site of attack by HCl.•The interaction is strong with binding energy of roughly 30 kJ mol−1.B3LYP, B3LYP-D3 and MP2 calculations are used to predict the preferred site of binding of HCl to temozolomide (TMZ). Binding energies, bond length perturbations, and infrared spectra of the various heterodimers indicate that the O-atom of the terminal amide group is the preferred attack site. The interaction is strong with binding energy of roughly 30 kJ mol−1. The molecular electrostatic potential surrounding TMZ is consistent with this preference, but is unable to fully account for the energetic ordering of the other minima.
Co-reporter:Vincent de Paul N. Nziko and Steve Scheiner
The Journal of Organic Chemistry 2016 Volume 81(Issue 6) pp:2589-2597
Publication Date(Web):February 23, 2016
DOI:10.1021/acs.joc.6b00344
The combination of H2C═NH and cis-1,3-butadiene to form a six-membered ring was examined by quantum calculations. The energy barrier for this reaction is substantially lowered by the introduction of an imidazolium catalyst with either a H or halogen (X) atom in the 2-position, which acts via a H or halogen bond to the N atom of the imine, respectively. X = I has the largest effect, and Cl the smallest; Br and H are roughly equivalent. The catalyst retards the formation of the incipient N–C bond from imine to diene while simultaneously accelerating the C–C bond formation. The energy of the π* LUMO of the imine is lowered by the catalyst, which thereby enhances charge transfer from the diene to the imine. Assessment of free energies suggests catalytic rate acceleration by as much as 4–6 orders of magnitude.
Co-reporter:Okuma Emile Kasende, Vincent de Paul N. Nziko and Steve Scheiner
The Journal of Physical Chemistry B 2016 Volume 120(Issue 35) pp:9347-9361
Publication Date(Web):August 11, 2016
DOI:10.1021/acs.jpcb.6b06150
Temozolomide (TMZ) was paired with each of the five nucleic acid bases, and the potential energy surface searched for all minima, in the context of dispersion-corrected density functional theory and MP2 methods. Three types of arrangements were observed, with competitive stabilities. Coplanar H-bonding structures, reminiscent of Watson–Crick base pairs were typically the lowest in energy, albeit by a small amount. Also very stable were perpendicular arrangements that included one or more H-bonds. The two monomers were stacked approximately parallel to one another in the third category, some of which contained weak and distorted H-bonds. Dispersion was found to be a dominating attractive force, largest for the stacked structures, and smallest for the coplanar dimers.
Quantum calculations are used to measure the binding of halides to a number of bipodal dicationic receptors, constructed as a pair of binding units separated by a spacer group. A number of variations are studied. A H atom on each binding unit (imidazolium or triazolium) is replaced by Br or I. Benzene, thiophene, carbazole, and dimethylnaphthalene are considered as spacer groups. Each receptor is paired with halides F−, Cl−, Br−, and I−. Substitution with I on the binding unit yields a large enhancement of binding, as much as 13 orders of magnitude; a much smaller increase occurs for substitution with Br. Imidazolium is a more effective binding agent than is triazolium. Benzene and dimethylnaphthalene represent the best spacers, followed by thiophene and carbazole. F− binds much more strongly than do the other halides, which obey the order Cl−>Br−>I−.
The Journal of Organic Chemistry 2016 Volume 81(Issue 10) pp:4316-4324
Publication Date(Web):May 2, 2016
DOI:10.1021/acs.joc.6b00755
Quantum calculations are used to study the manner in which quinones interact with proton-donating molecules. For neutral donors, a stacked geometry is favored over a H-bond structure. The former is stabilized by charge transfers from the N or O lone pairs to the quinone’s π* orbitals. Following the addition of an electron to the quinone, the radical anion forms strong H-bonded complexes with the various donors. The presence of the donor enhances the electron affinity of the quinone. This enhancement is on the order of 15 kcal/mol for neutral donors, but up to as much as 85 kcal/mol for a cationic donor. The increase in electron affinity is larger for electron-rich quinones than for their electron-deficient counterparts, containing halogen substituents. Similar trends are in evidence when the systems are immersed in aqueous solvent.
Quantum calculations are used to examine whether an AH⋅⋅⋅D H-bond is unambiguously verified by a downfield shift of the bridging proton's NMR signal or a red (or blue) shift of the AH stretching frequency in the IR spectrum. It is found that such IR band shifts will occur even if the two groups experience weak or no attractive force, or if they are drawn in so close together that their interaction is heavily repulsive. The mere presence of a proton-acceptor molecule can affect the chemical shielding of a position occupied by a protondonor by virtue of its electron density, even if there is no H-bond present. This density-induced shielding is heavily dependent on position around the proton–acceptor atom, and varies from one group to another. Evidence of a hydrogen bond rests on the measurement of a proton deshielding in excess of what is caused purely by the presence of the proton acceptor species.
Co-reporter:Vincent de Paul N. Nziko and Steve Scheiner
The Journal of Organic Chemistry 2015 Volume 80(Issue 20) pp:10334-10341
Publication Date(Web):September 25, 2015
DOI:10.1021/acs.joc.5b01985
The interaction between thiourea and a series of imines was examined via high-level ab initio calculations. For each imine, there is a set of stable complexes that represent minima on the potential energy surface. One type is characterized by a pair of symmetric NH···N hydrogen bonds (HBs), with both NH groups of thiourea approaching the imine N from above and below its molecular plane. Another geometry category combines a linear NH···N with a CH···S HB. A third, which is less stable, has the S approaching the imine’s CH2 group, and a stacking arrangement is present in the fourth. Interaction energies vary from ∼2 kcal/mol to a maximum of 13.5 kcal/mol. The formation of the complex tends to elongate the C–N bond within the imine by as much as 0.004 Å, but there are certain dimers that cause a small contraction of this bond.
Co-reporter:Vincent de Paul N. Nziko and Steve Scheiner
The Journal of Physical Chemistry A 2015 Volume 119(Issue 22) pp:5889-5897
Publication Date(Web):May 13, 2015
DOI:10.1021/acs.jpca.5b03359
SF2 and SF4 were each paired with a series of unsaturated hydrocarbons including ethene, ethyne, 1,3-butadiene, and benzene, in each case forming a chalcogen bond between the S atom and the carbon π-system. MP2 ab initio calculations reveal that the S atom is situated directly above one specific C═C bond, even when more than one are present. The binding energies range between 3.3 and 6.6 kcal/mol. SF2 engages in a stronger, and shorter, noncovalent bond than does SF4 for all systems with the exception of benzene, to which SF4 is more tightly bound. cis-Butadiene complexes contain the shortest chalcogen bond, even if not necessarily the strongest. The internal S–F covalent bonds elongate upon formation of each chalcogen bond. The molecules are held together largely by charge transfer forces, particularly from the C═C π-bonds to the σ*(SF) antibonding orbitals. In the case of SF2, a sulfur lone pair can transfer charge into the π* MOs of the alkene, a back-transfer which is more difficult for SF4.
The Journal of Physical Chemistry A 2015 Volume 119(Issue 52) pp:13064-13073
Publication Date(Web):December 9, 2015
DOI:10.1021/acs.jpca.5b09738
The effects of substituent and overall charge upon the binding of a halide anion by a bis(triazolium) receptor are studied by M06-2X DFT calculations, with the aug-cc-pVDZ basis set. Comparison is also made between a receptor that engages in H-bonds, with a halogen-bonding species. Fluoride is clearly most strongly bound, followed by Cl–, Br–, and I– in that order. The dicationic receptor engages in stronger complexes, but not by a very wide margin compared to its neutral counterpart. The binding is enhanced as the substituent on the two triazolium rings becomes progressively more electron-withdrawing. Halogen-substituted receptors, whether neutral or cationic, display a greater sensitivity to substituent than do their H-bonding counterparts. Both Coulombic and charge transfer factors obey the latter trends but do not correctly reproduce the stronger halogen vs hydrogen bonding. Both H-bonds and halogen bonds are nearly linear within the complexes, due in part to bond rotations within the receptor that bring the two triazole rings closer to coplanarity with the central benzene ring.
Chemistry - A European Journal 2015 Volume 21( Issue 4) pp:1474-1481
Publication Date(Web):
DOI:10.1002/chem.201404970
Abstract
CF3H as a proton donor was paired with a variety of anions, and its properties were assessed by MP2/aug-cc-pVDZ calculations. The binding energy of monoanions halide, NO3−, formate, acetate, HSO4−, and H2PO4− lie in the 12–17 kcal mol−1 range, although F− is more strongly bound, by 26 kcal mol−1. Dianions SO42− and HPO42− are bound by 27 kcal mol−1, and trianion PO43− by 45 kcal mol−1. When two O atoms are available on the anion, the CH⋅⋅⋅O− H-bond (HB) is usually bifurcated, although asymmetrically. The CH bond is elongated and its stretching frequency redshifted in these ionic HBs, but the shift is reduced in the bifurcated structures. Slightly more than half of the binding energy is attributed to Coulombic attraction, with smaller contributions from induction and dispersion. The amount of charge transfer from the anions to the σ*(CH) orbital correlates with many of the other indicators of bond strength, such as binding energy, CH bond stretch, CH redshift, downfield NMR spectroscopic chemical shift of the bridging proton, and density at bond critical points.
The Journal of Physical Chemistry A 2015 Volume 119(Issue 34) pp:9189-9199
Publication Date(Web):August 7, 2015
DOI:10.1021/acs.jpca.5b06831
The ability of neutral and charged S-compounds to form different sorts of noncovalent bonds is examined by ab initio calculations. Neutrals are represented by CH3SH and fluoro-substituted FSCH3; cations are (CH3)3S+, CH3SH2+, and FHSCH3+. Each is paired with N-methylacetamide (NMA) whose O atom serves as a common electron donor. Charged species engage in much stronger noncovalent bonds than do the neutral molecules, by as much as an order of magnitude. The strongest noncovalent bond for any system is a O···SF chalcogen bond wherein the O lies directly opposite a S–F covalent bond, amounting to as much as 39 kcal/mol. Second in binding energy is the SH···O H-bond, which can be as large as 34 kcal/mol. Somewhat weaker is the O···SC chalcogen bond, followed by the CH···O H-bond and finally the O···C tetrel bond, which has the appearance of a trifurcated H-bond. Any CH group that participates in a CH···O H-bond shifts its NMR signal downfield by an amount roughly proportional to the strength of the H-bond. This situation is clearly distinguishable from that in a O···S chalcogen or SH···O H-bond wherein the methyl protons are shifted upfield.
Co-reporter:Luis Miguel Azofra, Ibon Alkorta, and Steve Scheiner
The Journal of Physical Chemistry A 2015 Volume 119(Issue 3) pp:535-541
Publication Date(Web):December 29, 2014
DOI:10.1021/jp511828h
SOF2, SOFCl, and SOCl2 were each paired with a series of N bases. The potential energy surface of the binary complexes were characterized by MP2 calculations with double and triple-ξ basis sets, extrapolated to complete sets. The most stable configurations contained a S···N chalcogen bond with interaction energies as high as 6.8 kcal/mol. These structures are stabilized by a Nlp → σ*(S–Z) electron transfer (Z = O, F, Cl), complemented by Coulombic attraction of N to the σ-hole opposite the Z atom. N···S–F and N···S–Cl chalcogen bonds are stronger than N···S═O interactions. Formation of each chalcogen bond elongates all of the internal covalent bonds within SOXY, especially the S–Cl bond. Halogen-bonded (N···Cl–S) complexes were also observed, but these are more weakly bound, by less than 3 kcal/mol.
Chemistry - A European Journal 2015 Volume 21( Issue 38) pp:13330-13335
Publication Date(Web):
DOI:10.1002/chem.201501921
Abstract
The binding of F−, Cl−, Br−, and I− anions by bis-triazole-pyridine (BTP) was examined by quantum chemical calculations. There is one H atom on each of the two triazole rings that chelate the halide via H bonds. These H atoms were replaced by halogens Cl, Br, and I, thus substituting H bonds by halogen bonds. I substitution strongly enhances the binding; Br has a smaller effect, and Cl weakens the interaction. The strength of the interaction is sensitive to the overall charge on the BTP, rising as the binding agent becomes singly and then doubly positively charged. The strongest preference of a halide for halogenated as compared to unsubstituted BTP, as much as several orders of magnitude, is observed for I−. Both unsubstituted and I-substituted BTP could be used to selectively extract F− from a mixture of halides.
Co-reporter:Vincent de Paul N. Nziko and Steve Scheiner
The Journal of Organic Chemistry 2015 Volume 80(Issue 4) pp:2356-2363
Publication Date(Web):January 29, 2015
DOI:10.1021/acs.joc.5b00012
Density functional methods are used to examine the geometries and energetics of molecules containing a phenyl ring joined to the trigonal bipyramidal SF3 framework. The phenyl ring has a strong preference for an equatorial position. This preference remains when one or two ether −CH2OCH3 groups are added to the phenyl ring, ortho to SF3, wherein an apical structure lies nearly 30 kcal/mol higher in energy. Whether equatorial or apical, the molecule is stabilized by a S···O chalcogen bond, sometimes augmented by CH···F or CH···O H-bonds. The strength of the intramolecular S···O bond is estimated to lie in the range between 3 and 6 kcal/mol. A secondary effect of the S···O chalcogen bond is elongation of the S–F bonds. Solvation of the molecule strengthens the S···O interaction. Addition of substituents to the phenyl ring has only modest effects upon the S···O bond strength. A strengthening arises when an electron-withdrawing substituent is placed ortho to the ether and meta to SF3, while electron-releasing species produce an opposite effect.
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 11) pp:5142-5149
Publication Date(Web):27 Jan 2014
DOI:10.1039/C3CP55489A
Mixed dimers, trimers and tetramers composed of SO2 and CO2 molecules are examined by ab initio calculations to identify all minimum energy structures. While AIM formalism leads to the idea of a pair of C⋯O bonds in the most stable heterodimer, bound by some 2 kcal mol−1, NBO analysis describes the bonding in terms of charge transfer from O lone pairs of SO2 to the CO π* antibonding orbitals. The second minimum on the surface, just slightly less stable, is described by AIM as containing a single O⋯O chalcogen bond. The NBO picture is that of two transfers in opposite directions: one from a SO2 O lone pair to a π* antibond of CO2, supplemented by CO2 Olp → π*(SO). Decomposition of the interaction energies points to electrostatic attraction and dispersion as the dominant attractive components, in roughly equal measure. The various heterotrimers and tetramers generally retain the dimer structure as a starting point. Cyclic oligomers are favored over linear geometries, with a preference for complexes containing larger numbers of SO2 molecules.
Co-reporter:Luis Miguel Azofra, Ibon Alkorta and Steve Scheiner
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 35) pp:18974-18981
Publication Date(Web):29 Jul 2014
DOI:10.1039/C4CP02380C
The potential energy surfaces (PES) for the SO3:H2CO and (SO3)2:H2CO complexes were thoroughly examined at the MP2/aug-cc-pVDZ computational level. Heterodimers and trimers are held together primarily by S⋯O chalcogen bonds, supplemented by weaker CH⋯O and/or O⋯C bonds. The nature of the interactions is probed by a variety of means, including electrostatic potentials, AIM, NBO, energy decomposition, and electron density redistribution maps. The most stable dimer is strongly bound, with an interaction energy exceeding 10 kcal mol−1. Trimers adopt the geometry of the most stable dimer, with an added SO3 molecule situated so as to interact with both of the original molecules. The trimers are strongly bound, with total interaction energies of more than 20 kcal mol−1. Most such trimers show positive cooperativity, with shorter S⋯O distances, and three-body interaction energies of nearly 3 kcal mol−1.
Co-reporter:Okuma E. Kasende, Aristote Matondo, Mayaliwa Muzomwe, Jules Tshishimbi Muya, Steve Scheiner
Computational and Theoretical Chemistry 2014 Volume 1034() pp:26-31
Publication Date(Web):15 April 2014
DOI:10.1016/j.comptc.2014.02.005
•All possible binding sites of TMZ with water are considered, and binding energies evaluated.•The terminal amide group represents the strongest binding site, with water bound by 40 kJ/mol.•The global minimum is cyclic, with water acting as simultaneous proton donor and acceptor.•Molecular electrostatic potential (MEP) and Natural Bond Orbital (NBO) data aid in understanding the binding preferences.Computational methods are used to predict the most favorable site of temozolomide towards attack by a water molecule. The energetics of the various complexes are presented as well as their geometries, including perturbations of each subunit caused by the presence of the other. Molecular electrostatic potential and Natural Bond Orbital (NBO) data are used to understand the interactions which conclude the terminal amide group is the preferred attack site where water can act as simultaneous proton donor and acceptor. Other potential proton acceptor N atoms within the aromatic ring structure represent weaker binding sites. Some of the less strongly bound structures include a CH⋯O H-bond.Graphical abstract
The Journal of Physical Chemistry A 2014 Volume 118(Issue 17) pp:3183-3192
Publication Date(Web):April 10, 2014
DOI:10.1021/jp501449v
Neutral complexes containing a S···N chalcogen bond are compared with similar systems in which a positive charge has been added to the S-containing electron acceptor, using high-level ab initio calculations. The effects on both XS···N and XS+···N bonds are evaluated for a range of different substituents X = CH3, CF3, NH2, NO2, OH, Cl, and F, using NH3 as the common electron donor. The binding energy of XMeS···NH3 varies between 2.3 and 4.3 kcal/mol, with the strongest interaction occurring for X = F. The binding is strengthened by a factor of 2–10 in charged XH2S+···NH3 complexes, reaching a maximum of 37 kcal/mol for X = F. The binding is weakened to some degree when the H atoms are replaced by methyl groups in XMe2S+···NH3. The source of the interaction in the charged systems, like their neutral counterparts, is derived from a charge transfer from the N lone pair into the σ*(SX) antibonding orbital, supplemented by a strong electrostatic and smaller dispersion component. The binding is also derived from small contributions from a CH···N H-bond involving the methyl groups, which is most notable in the weaker complexes.
•Charge transfer from O lone pair to alkene π* antibonding orbital.•lp→π is most strongly bound complex type between H2O and perhalogenated alkenes.•Binding energies larger than 2 kcal/mol, insensitive to identity of halogen atoms.•Halogen-bonded complexes are slightly less stable, followed by OH⋯X H-bond.A thorough search of the potential energy surface is carried out for heterodimers of water with C2ClnF4−n. Three different types of interactions are observed. Structures dominated by a lone pair–π interaction have the highest binding energies, and are stabilized by charge transfer from O lone pairs of H2O to the CC π* antibonding orbital of the alkene. Halogen-bonded O⋯Cl complexes are slightly less strongly bound, followed by OH⋯X hydrogen bonds. The replacements of Cl by F atoms have only small effects upon binding energies. Inclusion of vibrational and entropic effects removes the clear energetic superiority of lp–π binding energies. When combined with the observation of several similar geometries for each particular heterodimer type, and a sensitivity to basis set, it would be quite difficult to predict with any degree of certainty the single most stable configuration, even with very high level calculations.Graphical abstract
The Journal of Physical Chemistry A 2014 Volume 118(Issue 21) pp:3835-3845
Publication Date(Web):May 2, 2014
DOI:10.1021/jp501932g
The SO2 molecule is paired with a number of carbonyl-containing molecules, and the properties of the resulting complexes are calculated by high-level ab initio theory. The global minimum of each pair is held together primarily by a S···O chalcogen bond wherein the lone pairs of the carbonyl O transfer charge to the π* antibonding SO orbital, supplemented by smaller contributions from weak CH···O H-bonds. The binding energies vary between 4.2 and 8.6 kcal/mol, competitive with even some of the stronger noncovalent forces such as H-bonds and halogen bonds. The geometrical arrangement places the carbonyl O atom above the plane of the SO2 molecule, consistent with the disposition of the molecular electrostatic potentials of the two monomers. This S···O bond differs from the more commonly observed chalcogen bond in both geometry and origin. Substituents exert their influence via inductive effects that change the availability of the carbonyl O lone pairs as well as the intensity of the negative electrostatic potential surrounding this atom.
The Journal of Physical Chemistry A 2014 Volume 118(Issue 40) pp:9575-9587
Publication Date(Web):September 7, 2014
DOI:10.1021/jp5070598
The CH···π hydrogen bonds (HBs) between trimethylamine (TMA) and an assortment of π-systems are generally weaker than those in which CF3H serves as a proton donor, despite the larger number of CH groups available to serve as donors in the amine. The added positive charge of tetramethylammonium (TMA+) enhances the binding energy by a factor between 4 and 7. The strongest such interaction for TMA+ occurs with indole, bound by 15.5 kcal/mol. Changing from ionic CH···π to NH···π further strengthens the interaction. Conjugation of the π-system improves its proton-accepting capacity, which is further enhanced by aromaticity. Dispersion plays a major role in CH···π HBs: It is the prime contributor in the neutral HBs of TMA, and comparable to Coulombic forces for CF3H and even in ionic CH···π HBs of TMA+. Many of the results can be understood on the basis of a combination of electrostatic potentials and charge transfers.
Co-reporter:Vincent de Paul N. Nziko and Steve Scheiner
The Journal of Physical Chemistry A 2014 Volume 118(Issue 45) pp:10849-10856
Publication Date(Web):October 22, 2014
DOI:10.1021/jp509212t
The N···S chalcogen bond between SF4 and a series of alkyl and arylamines is examined via ab initio calculations. This bond is a strong one, with a binding energy that varies from a minimum of 7 kcal/mol for NH3 to 14 kcal/mol for trimethylamine. Its strength derives in large measure from charge transfer from the N lone pair into the σ*(SF) antibonding orbitals involving the two equatorial F atoms, one of which is disposed directly opposite the N atom. Decomposition of the total interaction energy reveals that the induction energy constitutes more than half of the total attraction. The positive region of the molecular electrostatic potential of SF4 that lies directly opposite the equatorial F atoms is attracted to the N lone pair, but the magnitude of this negative region on each amine is a poor predictor of the binding energy. The shortness and strength of the N···S bond in the dimethylamine···SF4 complex suggest it may better be described as a weak covalent bond.
Accounts of Chemical Research 2013 Volume 46(Issue 2) pp:280
Publication Date(Web):November 7, 2012
DOI:10.1021/ar3001316
Among a wide range of noncovalent interactions, hydrogen (H) bonds are well known for their specific roles in various chemical and biological phenomena. When describing conventional hydrogen bonding, researchers use the notation AH···D (where A refers to the electron acceptor and D to the donor). However, the AH molecule engaged in a AH···D H-bond can also be pivoted around by roughly 180°, resulting in a HA···D arrangement. Even without the H atom in a bridging position, this arrangement can be attractive, as explained in this Account. The electron density donated by D transfers into a AH σ* antibonding orbital in either case: the lobe of the σ* orbital near the H atom in the H-bonding AH···D geometry, or the lobe proximate to the A atom in the HA···D case. A favorable electrostatic interaction energy between the two molecules supplements this charge transfer. When A belongs to the pnictide family of elements, which include phosphorus, arsenic, antimony, and bismuth, this type of interaction is called a pnicogen bond. This bonding interaction is somewhat analogous to the chalcogen and halogen bonds that arise when A is an element in group 16 or 17, respectively, of the periodic table.Electronegative substitutions, such as a F for a H atom opposite the electron donor atom, strengthen the pnicogen bond. For example, the binding energy in FH2P···NH3 greatly exceeds that of the paradigmatic H-bonding water dimer. Surprisingly, di- or tri-halogenation does not produce any additional stabilization, in marked contrast to H-bonds. Chalcogen and halogen bonds show similar strength to the pnicogen bond for a given electron-withdrawing substituent. This insensitivity to the electron-acceptor atom distinguishes these interactions from H-bonds, in which energy depends strongly upon the identity of the proton-donor atom.As with H-bonds, pnicogen bonds can extract electron density from the lone pairs of atoms on the partner molecule, such as N, O, and S. The π systems of carbon chains can donate electron density in pnicogen bonds. Indeed, the strength of A···π pnicogen bonds exceeds that of H-bonds even when using strong proton donors such as water with the same π system.H-bonds typically have a high propensity for a linear AH···D arrangement, but pnicogen bonds show an even greater degree of anisotropy. Distortions of pnicogen bonds away from their preferred geometry cause a more rapid loss of stability than in H-bonds. Although often observed in dimers in the gas phase, pnicogen bonds also serve as the glue in larger aggregates, and researchers have found them in a number of diffraction studies of crystals.
It is well known that noncovalent bonds are weakened when stretched from their equilibrium intermolecular separation. Quantum chemical calculations are used to examine and compare the sensitivity to stretches of hydrogen, halogen, chalcogen, and pnicogen bonds. NH3 was taken as the universal electron donor, paired with HOH and FH in H-bonds, as well as with FPH2, FSH, and FCl. Even though the binding energies span a wide range, stretching the intermolecular separation by 1 Å cuts this quantity by the same proportion, roughly in half, for each system. Taking the sum of van der Waals radii as an arbitrary cutoff, the H-bond energy in FH⋯NH3 remains at 5.5 kcal mol−1 while the binding energy of the other three bond types is only slightly smaller at 4.5–4.7 kcal mol−1.
The Journal of Physical Chemistry B 2013 Volume 117(Issue 39) pp:11575-11583
Publication Date(Web):September 12, 2013
DOI:10.1021/jp406326h
The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. However, the stability of this structure is highly dependent upon interpeptide H-bonds with the second chain. The latter forces include not only the usual NH···O interaction, but also a pair of CH···O H-bonds. The secondary minimum is also of C7 type and likewise depends in part upon CH···O H-bonds for its stability. The latter interactions also play a part in the tertiary minimum. A two-strand β-sheet structure is not yet in evidence for this small model system, requiring additional peptide units to be added to each chain.
The Journal of Physical Chemistry A 2013 Volume 117(Issue 40) pp:10551-10562
Publication Date(Web):September 12, 2013
DOI:10.1021/jp4081788
Quantum calculations find that neutral methylamines and thioethers form complexes, with N-methylacetamide (NMA) as proton acceptor, with binding energies of 2–5 kcal/mol. This interaction is magnified by a factor of 4–9, bringing the binding energy up to as much as 20 kcal/mol, when a CH3+ group is added to the proton donor. Complexes prefer trifurcated arrangements, wherein three separate methyl groups donate a proton to the O acceptor. Binding energies lessen when the systems are immersed in solvents of increasing polarity, but the ionic complexes retain their favored status even in water. The binding energy is reduced when the methyl groups are replaced by longer alkyl chains. The proton acceptor prefers to associate with those CH groups that are as close as possible to the S/N center of the formal positive charge. A single linear CH··O hydrogen bond (H-bond) is less favorable than is trifurcation with three separate methyl groups. A trifurcated arrangement with three H atoms of the same methyl group is even less favorable. Various means of analysis, including NBO, SAPT, NMR, and electron density shifts, all identify the +CH··O interaction as a true H-bond.
The Journal of Physical Chemistry A 2013 Volume 117(Issue 2) pp:489-496
Publication Date(Web):December 28, 2012
DOI:10.1021/jp310942u
The natural and fundamental proclivities of interaction between a pair of peptide units are examined using high-level ab initio calculations. The NH···O H-bonded structure is found to be the most stable configuration of the N-methylacetamide (NMA) model dimer, but only slightly more so than a stacked arrangement. The H-bonded geometry is destabilized by only a small amount if the NH group is lifted out of the plane of the proton-accepting amide. This out-of-plane motion is facilitated by a stabilizing charge transfer from the CO π bond to the NH σ* antibonding orbital. The parallel and antiparallel stacked dimers are nearly equal in energy, both only slightly less stable than the NH···O H-bonded structure. Both are stabilized by a combination of CH···O H-bonding and a π→π* transfer between the two CO bonds. There are no minima on the surface that are associated with Olp→π*(CO) transfers, due in large part to strong electrostatic repulsion between the two O atoms, which resists an approach of a carbonyl O from above the C═O bond of the other amide.
Co-reporter:Christopher R. Jones ; Pranjal K. Baruah ; Amber L. Thompson ; Steve Scheiner ;Martin D. Smith
Journal of the American Chemical Society 2012 Volume 134(Issue 29) pp:12064-12071
Publication Date(Web):July 12, 2012
DOI:10.1021/ja301318a
Whether nonconventional hydrogen bonds, such as the C–H···O interaction, are a consequence or a determinant of conformation is a long-running and unresolved issue. Here we outline a solid-state and quantum mechanical study designed to investigate whether a C–H···O interaction can override the significant trans-planar conformational preferences of α-fluoroamide substituents. A profound change in dihedral angle from trans-planar(OCCF) to cis-planar(OCCF) observed on introducing an acceptor group for a C–H···O hydrogen bond is consistent with this interaction functioning as a determinant of conformation in certain systems. This testifies to the potential influence of the C–H···O hydrogen bond and is consistent with the assignment of this interaction as a contributor to overall conformation in both model and natural systems.
Chemical Physics Letters 2012 Volume 532() pp:31-35
Publication Date(Web):12 April 2012
DOI:10.1016/j.cplett.2012.02.064
Abstract
Pnicogen, chalcogen, and halogen atoms have been shown previously to have some elements in common with H-bonds, including charge transfer into a σ∗ antibonding orbital. While H-bonds are known to have a strong propensity toward linearity, there is little known about the angular sensitivity of the former interactions. Ab initio calculations are performed that show that the noncovalent bonds formed between P, S, and Cl atoms with a N electron donor are strongly anisotropic, more sensitive to angular distortion than are H-bonds. Energy decomposition implicates exchange repulsion as the force that is chiefly responsible for this pattern.
Chemical Physics Letters 2012 Volume 536() pp:30-33
Publication Date(Web):21 May 2012
DOI:10.1016/j.cplett.2012.03.085
Abstract
The effects of carbon chains placed on the electron-accepting P atom of a P⋯N bond are examined via ab initio calculations. Saturated alkyl groups have a mild weakening effect, regardless of chain length. In contrast, incorporation of double bonds into the chain strengthens the interaction, CC triple bonds even more so. These effects are only slightly enhanced by additional conjugated double bonds or an aromatic ring. Placing F atoms onto the carbon chains strengthens the P⋯N bond, but only by a small amount, which wanes as the F atom is displaced further from the P along the chain.
The Journal of Physical Chemistry A 2012 Volume 116(Issue 13) pp:3487-3497
Publication Date(Web):March 6, 2012
DOI:10.1021/jp301288e
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 = CH3 < NH2 < CF3 < OH < Cl < NO2 < F. However, there is some variability in this pattern, particularly for the NO2 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.
N-Methylacetamide, a model of the peptide unit in proteins, is allowed to interact with CH3SH, CH3SCH3, and CH3SSCH3 as models of S-containing amino acid residues. All of the minima are located on the ab initio potential energy surface of each heterodimer. Analysis of the forces holding each complex together identifies a variety of different attractive forces, including SH⋅⋅⋅O, NH⋅⋅⋅S, CH⋅⋅⋅O, CH⋅⋅⋅S, SH⋅⋅⋅π, and CH⋅⋅⋅π H-bonds. Other contributing noncovalent bonds involve charge transfer into σ* and π* antibonds. Whereas some of the H-bonds are strong enough that they represent the sole attractive force in several dimers, albeit not usually in the global minimum, charge-transfer-type noncovalent bonds play only a supporting role. The majority of dimers are bound by a collection of several of these attractive interactions. The SH⋅⋅⋅O and NH⋅⋅⋅S H-bonds are of comparable strength, followed by CH⋅⋅⋅O and CH⋅⋅⋅S.
Physical Chemistry Chemical Physics 2011 vol. 13(Issue 31) pp:13860-13872
Publication Date(Web):13 May 2011
DOI:10.1039/C1CP20427K
Whereas CH⋯O H-bonds are usually weaker than interpeptide NH⋯O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH⋯O are surprisingly strong, comparable to, and in some cases stronger than, the NH⋯O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH⋯N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P⋯N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P–H σ* antibond that characterizes the PH⋯N H-bond.
The attractive noncovalent interaction of a P atom with N is derived primarily from two sources. Charge transfer from the N lone pair into the σ∗ antibonding orbital of a P–X bond that is turned away from the N atom combines with attractive Coulombic forces. As in the case of H-bonding, which is parallel in some ways to P⋯N attraction, placement of an electron-withdrawing substituent on the P atom enhances both of these components, and strengthens the overall interaction. However, in stark contrast with H-bonding, halogenation beyond monosubstitution does not lead to any further strengthening of the P⋯N noncovalent bond. Indeed, di and tri-substitution lead to small reductions in the interaction energy. In all cases, the geometry which contains a P⋯N bond is more stable than other candidate structures, some of which contain hydrogen or halogen bonds.
The Journal of Physical Chemistry A 2011 Volume 115(Issue 40) pp:11101-11110
Publication Date(Web):September 8, 2011
DOI:10.1021/jp2082787
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. The present work considers whether other atoms, namely, O and S, can also participate as electron donors, and in which bonding environments. Also considered are the π-systems of multiply bonded C atoms. Unlike an earlier observation that the interaction is unaffected by the nature of the electron-acceptor atom, there is strong sensitivity to the donor. The P···D binding energy diminishes in the order D = NH3 > H2CO > H2CS > H2O > H2S, different from the patterns observed in both H and halogen bonds. The P···D interactions are comparable to, and in some cases stronger than, the analogous H-bonds formed by HOH as proton donor. The carbon π systems form surprisingly strong P···D complexes, augmented by the back-donation from the P lone pair to the C–C π* antibond, which surpass the strengths of H-bonds, even some with HF as proton donor.
The Journal of Physical Chemistry A 2011 Volume 115(Issue 41) pp:11202-11209
Publication Date(Web):July 5, 2011
DOI:10.1021/jp203964b
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 FH2P···N(CH3)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.
Journal of the American Chemical Society 2010 Volume 132(Issue 46) pp:16450-16459
Publication Date(Web):November 3, 2010
DOI:10.1021/ja105204v
Ab initio and density functional theory calculations are used to monitor the process wherein a OH· radical is allowed to approach the various CH groups of a Leu dipeptide, with its CH2CH(CH3)2 side chain. After forming an encounter complex, the OH· abstracts the pertinent H atom, and the resulting HOH is then dissociated from the complex. The energy barriers for H· abstraction from the β, γ, and δ CH groups are all less than 8 kcal/mol, but a significantly higher barrier is computed for the CαH removal. This higher barrier is the result of the strong H-bonds formed in the encounter complex between the OH· and the NH and C═O groups of the peptide units that surround the Cα atom. This low-energy complex represents a kinetic trap which raises the energy needed to surmount the ensuing H· transfer barrier.
Journal of Molecular Structure 2010 Volume 976(1–3) pp:49-55
Publication Date(Web):15 July 2010
DOI:10.1016/j.molstruc.2009.10.045
A glycine dipeptide is paired with one or more formamide molecules in a variety of different H-bonding configurations, monitoring the structural and spectroscopic features of the dipeptide via ab initio calculations. Of particular interest is the way in which the perturbations induced by a CH⋯O H-bond between the dipeptide and a proton acceptor are themselves affected by the presence of other H-bonds to the dipeptide. It is found that whether or not these other H-bonds are present, the introduction of a CH⋯O H-bond causes the C–H bond to shorten, and its stretching frequency is shifted to the blue. Also relatively unaffected is the NMR chemical shift of the CH proton which moves further downfield upon formation of the CH⋯O H-bond. In contrast, the effect of this CH⋯O H-bond upon the NH group of the dipeptide varies depending on whether or not there are other H-bonds present. Specific effects of cooperativity are less amenable to simple interpretation in that there are differences in behavior between the two conformations of the dipeptide examined.
Israel Journal of Chemistry 2009 Volume 49( Issue 2) pp:139-147
Publication Date(Web):
DOI:10.1560/IJC.49.2.139
Abstract
The transfer of a proton across a hydrogen bond can be influenced by a number of factors, including H-bond length, intramolecular angles, and the presence of neighboring groups. The ability of different factors to push a proton across the H-bond is examined for a specific and very important pair of catalytic groups, Ser-195 and His-57, within the context of a serine proteinase enzyme. The influence of residue Asp-102 is considered for different charge states, as is the nature of the surrounding medium. Also examined are the perturbations introduced by the substrate and external ions and dipoles.
Co-reporter:Mingxiu Liu, Qingzhong Li and Steve Scheiner
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 7) pp:NaN5559-5559
Publication Date(Web):2017/01/30
DOI:10.1039/C6CP07531B
Ab initio calculations have been performed for the complexes H+–PyTX3⋯NH3 and H+–furanTF3⋯NH3 (T = C, Si, and Ge; X = F and Cl) with focus on geometries, energies, orbital interactions, and electron densities to study the influence of protonation on the strength of tetrel bonding. The primary interaction mode between α/β-furanCF3/p-PyCF3 and NH3 changes from an F⋯H hydrogen bond to a C⋯N tetrel bond as a result of protonation. Importantly, the protonation has a prominent enhancing effect on the strength of tetrel bonding with an increase in binding energy from 14 to 30 kcal mol−1. The tetrel bonding becomes stronger in the order H+–p-PySiF3⋯NH3 < H+–m-PySiF3⋯NH3 < H+–o-PySiF3⋯NH3, showing a reverse trend from that of the neutral analogues. In addition, there is competition between the tetrel and hydrogen bonds in the protonated complexes, in which the hydrogen bond is favored in the complexes of H+–p-PyCF3 but the tetrel bond is preferred in the complexes of H+–p-PyTX3 (T = Si, Ge; X = F, Cl) and H+–o/m-PySiF3.
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 11) pp:NaN5149-5149
Publication Date(Web):2014/01/27
DOI:10.1039/C3CP55489A
Mixed dimers, trimers and tetramers composed of SO2 and CO2 molecules are examined by ab initio calculations to identify all minimum energy structures. While AIM formalism leads to the idea of a pair of C⋯O bonds in the most stable heterodimer, bound by some 2 kcal mol−1, NBO analysis describes the bonding in terms of charge transfer from O lone pairs of SO2 to the CO π* antibonding orbitals. The second minimum on the surface, just slightly less stable, is described by AIM as containing a single O⋯O chalcogen bond. The NBO picture is that of two transfers in opposite directions: one from a SO2 O lone pair to a π* antibond of CO2, supplemented by CO2 Olp → π*(SO). Decomposition of the interaction energies points to electrostatic attraction and dispersion as the dominant attractive components, in roughly equal measure. The various heterotrimers and tetramers generally retain the dimer structure as a starting point. Cyclic oligomers are favored over linear geometries, with a preference for complexes containing larger numbers of SO2 molecules.
Physical Chemistry Chemical Physics 2016 - vol. 18(Issue 27) pp:NaN18023-18023
Publication Date(Web):2016/06/13
DOI:10.1039/C6CP03771B
Quantum calculations examine how the NH⋯Y H-bond compares to the equivalent NX⋯Y halogen bond, as well as to comparable CH/CX donors. Succinimide and saccharin, and their corresponding halogen-substituted derivatives, are chosen as the prototype NH/NX donors, paired with a wide range of electron donor molecules. The NH⋯Y H-bond is weakened if the bridging H is replaced by Cl, and strengthened by I; a Br halogen bond is roughly comparable to a H-bond. The lone pairs of the partner molecule are stronger electron donors than are π-systems. Whereas Coulombic forces represent the largest fraction of the attractive force in the H-bonds, induction energy is magnified in the halogen bonds, surpassing electrostatics in several cases. Mutation of NH/NX to CH/CX weakens the binding energy to roughly half its original value, while also lengthening the intermolecular distances by 0.3–0.8 Å.
Co-reporter:Vincent de Paul N. Nziko and Steve Scheiner
Physical Chemistry Chemical Physics 2016 - vol. 18(Issue 5) pp:NaN3590-3590
Publication Date(Web):2016/01/05
DOI:10.1039/C5CP07545A
In addition to the standard halogen bond formed when NH3 approaches XCN (X = F, Cl, Br, I) along its molecular axis, a perpendicular approach is also possible, toward a π-hole that is present above the X–C bond. MP2/aug-cc-pVDZ calculations indicate the latter geometry is favored for X = F, and the σ-hole structure is preferred for the heavier halogens. The π-hole structure is stabilized by charge transfer from the NH3 lone pair into the π*(CN) antibonding orbital, and is characterized by a bond path from the N of NH3 to the C atom of XCN, a form of tetrel bond. The most stable 2:1 NH3/XCN heterotrimer for X = F and Cl is cyclic and contains a tetrel bond augmented by a pair of NH⋯N H-bonds. For X = Br and I, the favored trimer is noncyclic, stabilized by a tetrel and a halogen bond.
Physical Chemistry Chemical Physics 2011 - vol. 13(Issue 31) pp:NaN13872-13872
Publication Date(Web):2011/05/13
DOI:10.1039/C1CP20427K
Whereas CH⋯O H-bonds are usually weaker than interpeptide NH⋯O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH⋯O are surprisingly strong, comparable to, and in some cases stronger than, the NH⋯O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH⋯N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P⋯N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P–H σ* antibond that characterizes the PH⋯N H-bond.
![DITHIENO[3,2-B:3',2'-E]THIOPHENE 4,4-DIOXIDE](http://img.cochemist.com/ccimg/3900/3807-53-2.png)
![DITHIENO[3,2-B:3',2'-E]THIOPHENE 4,4-DIOXIDE](http://img.cochemist.com/ccimg/3900/3807-53-2_b.png)
![Dithieno[3,2-b:2',3'-d]thiophene](/data/chemimg/25800/3593-75-7.png)
![Dithieno[3,2-b:2',3'-d]thiophene](/data/chemimg/25800/3593-75-7_b.png)
