N?H···S and S?H···N intramolecular hydrogen bond in β‐thioaminoacrolein: A quantum chemical study

The conformational study of β‐thioaminoacrolein was performed at various theoretical levels, HF, B3LYP, and MP2 with 6‐311++G(d,p) basis set, and the equilibrium conformations were determined. To have more reliable energies, the total energies of all conformers were recomputed at high‐level ab initio methods, G2MP2, G3, and CBS‐QB3. According to these calculations, the intramolecular hydrogen bond is accepted as the origin of conformational preference in thialamine (TAA) and thiolimine groups. The hydrogen bond strength in various resonance‐assisted hydrogen bond systems was evaluated by HB energy, geometrical parameters, topological parameters, and charge transfers corresponding to orbital interactions. Furthermore, our results reveal that the TAA tautomer has extra stability with respect to the other tautomers. The population analyses of the possible conformations by NBO predict that the origin of this preference is mainly due to the π‐electron delocalization in framework of TAA forms, especially usual π_C?C → π*_C?S and Lp (N) → π*_C?C charge transfers. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Characterization of the N?H···ON and N?H···NO H‐bonds in nitrosamine dimers

Ab initio molecular orbital and DFT calculations have been carried out for three most stable dimers of parent nitrosamine (NA) in order to elucidate the structures and energetics of the dimers. The structures were optimized using HF, B3LYP, and MP2 methods with 6‐311+G(d,p) and 6‐311++G(2d,2p) basis sets. At the optimized geometries obtained at MP2/6‐311++G(2d,2p) level of theory, the energies were evaluated at QCISD/aug‐cc‐pVDZ and CCSD/aug‐cc‐pVDZ levels. The most stable dimer has two N? H···O?N hydrogen bonds and the least stable dimer has two N? H···N?O hydrogen bonds. The natural bond orbital analysis showed that the lpO(N) → BD*(N? N) and lpO(N) → BD*(N? H_b) interactions play a decisive role in the stabilization of the NH···O(N) hydrogen bonds in dimers. The atoms in molecules results reveal that the intermolecular N? H···O(N) H‐bonds in dimers have electrostatic character. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Intermolecular interactions in group 14 hydrides: Beyond C?H···H?C contacts

In line with previous work in which we established the factors that enhance attractive C? H···H? C dihydrogen interactions in alkanes, an extended theoretical analysis of noncovalent intermolecular interactions in group 14 hydrides is presented here. Remarkably, these weak interactions may play a major role in determining the crystal structures adopted by several families of molecules. A combined structural and computational analysis at the MP2 level allowed us to identify and characterize different interactions of the type E? H···H? E and E···H? E (E = Si, Ge, Sn, and Pb), and to find also the most suitable scenario for the establishment of each particular type. The nature of the interactions has been analyzed in terms of natural charges of the atoms involved and a topological analysis of the electron density of several dimers confirms the existence of H···H and H···E attractive contacts. We have observed that the interaction strength increases when descending down the periodic group and that silicon has a marked tendency to establish Si···H? Si interactions. A size‐dependent backbone effect that reinforces H···H dihydrogen interactions in polyhedral systems has also been found.     

A new unconventional halogen bond C?X···H?M between HCCX (X = Cl and Br) and HMH (M = Be and Mg): An ab initio study

In this article, a new type of halogen‐bonded complex YCCX···HMY (X = Cl, Br; M = Be, Mg; Y = H, F, CH₃) has been predicted and characterized at the MP2/aug‐cc‐pVTZ level. We named it as halogen‐hydride halogen bonding. In each YCCX···HMY complex, a halogen bond is formed between the positively charged X atom and the negatively charged H atom. This new kind of halogen bond has similar characteristics to the conventional halogen bond, such as the elongation of the C? X bond and the red shift of the C? X stretch frequency upon complexation. The interaction strength of this type of halogen bond is in a range of 3.34–10.52 kJ/mol, which is smaller than that of dihydrogen bond and conventional halogen bond. The nature of the electrostatic interaction in this type of halogen bond has also been unveiled by means of the natural bond orbital, atoms in molecules, and energy decomposition analyses. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Investigation on the individual contributions of N?H···OC and C?H···OC interactions to the binding energies of β‐sheet models

In this article, the binding energies of 16 antiparallel and parallel β‐sheet models are estimated using the analytic potential energy function we proposed recently and the results are compared with those obtained from MP2, AMBER99, OPLSAA/L, and CHARMM27 calculations. The comparisons indicate that the analytic potential energy function can produce reasonable binding energies for β‐sheet models. Further comparisons suggest that the binding energy of the β‐sheet models might come mainly from dipole–dipole attractive and repulsive interactions and VDW interactions between the two strands. The dipole–dipole attractive and repulsive interactions are further obtained in this article. The total of N? H···H? N and C?O···O?C dipole–dipole repulsive interaction (the secondary electrostatic repulsive interaction) in the small ring of the antiparallel β‐sheet models is estimated to be about 6.0 kcal/mol. The individual N? H···O?C dipole–dipole attractive interaction is predicted to be ?6.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?5.2 ± 0.6 kcal/mol in the parallel β‐sheet models. The individual C^α? H···O?C attractive interaction is ?1.2 ± 0.2 kcal/mol in the antiparallel β‐sheet models and ?1.5 ± 0.2 kcal/mol in the parallel β‐sheet models. These values are important in understanding the interactions at protein–protein interfaces and developing a more accurate force field for peptides and proteins. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

A novel single‐electron sodium bond system of H3C···Na?Y (YH,OH, F,CCH, CN,and NC)

A novel single‐electron sodium bond system of H₃C···Na? H (I), H₃C···Na? OH(II), H₃C···Na? F(III), H₃C···Na‐CCH(IV), H₃C···Na? CN (V) and H₃C···Na? NC (VI) complexes has been studied by using MP2/6‐311++G** and MP2/aug‐cc‐pVTZ methods for the first time. We demonstrated that the single‐electron sodium bond H₃C···Na? Y formed between H₃C and Na? Y (Y?H, OH, F, CCH, CN, and NC) could induce the Na? Y increased and stretching frequencies of I–IV and VI are red‐shifted, including the Na? N bond in complex V is blue‐shifted abnormally. The interaction energies are calculated at two levels of theory [MP2, CCSD(T)] with different basis. The results shows that the strength of binding bond in group 2 (IV–VI) with π electrons are stronger than that of group 1 (I–III) without π electrons. For all complexes, the main orbital interactions between moieties H₃C and Na? Y are LP₁(C)→LP*₁(Na). By comparisons with some related systems, it is concluded that the strength of single‐electron bond is increased in the order: hydrogen bond < bromine bond < sodium bond < lithium bond. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

On the reactivity of metal and organometallic halides toward R3Sn?O?SnR3 systems

Interaction of metallic salts (M = Hg, Sb, and Te) with bis(triorganotin)oxide, (R₃Sn)₂O, where (R = C₆H₅, p‐CH₃C₆H₄, and cyclo‐C₆H₁₁) at room temperature proceeded with the simultaneous cleavage of the Sn C and Sn O bonds, invariably yielding R₂SnO along with other products. Thus the treatment of HgX₂ (X = Cl, CN, SCN) with (R₃Sn)₂O resulted in the formation of polymeric diorganotin oxide R₂SnO along with R₃SnX and RHgX derivatives. The reaction of SbCl₃ with (R₃Sn)₂O was found to give R₂SnO, R₃SnCl, and RSbCl₂, whereas interaction with SbCl₅ provided R₂SnO, R₂SnCl₂, and R₂SbCl₃. Treatment of TeCl₄ with (R₃Sn)₂O provided R₂SnO, R₃SnCl, and RTeCl₃ at room temperature. At reflux temperature, reaction of PhTeCl₃ with (R₃Sn)₂O yielded R₂SnO, R₃SnCl, and mixed diorganotellurium dichloride, RPhTeCl₂. The course of reaction indicated the instability of Sn O Sn system proceeding via a four‐centered mechanism, providing organometallic compounds in profitable yield. © 2009 Wiley Periodicals, Inc. Heteroatom Chem 20:278–283, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20547     

Why is N···Be distance of NH3H+···DBeH shorter than that of NH3D+···HBeH? paradoxical geometrical isotope effects for partially isotope‐substituted dihydrogen‐bonded isotopomers

The partial isotope substitution for the change of geometrical parameters, interaction energies, and nuclear magnetic shielding tensors (σ) of dihydrogen‐bonded NH₃X⁺···YBeH (X, Y = H, D, and T) systems is analyzed. Based on the theoretical calculation, the distance between heavy atoms R_N···Be of NH₃H⁺···DBeH is clearly found to be shorter than that in NH₃D⁺···HBeH. Such apparently paradoxical geometrical isotope effect (GIE) on R_N···Be is revealed by the cooperative effect of two kinds of (1) primary covalent‐bonded GIE and (2) secondary dihydrogen‐bonded one. We have demonstrated that (1) the covalent bond lengths become shorter by heavier isotope‐substitution and (2) the dihydrogen‐bonded distance R_X···Y becomes shorter by heavier Y and lighter X isotope‐substitution due to the difference of electronic structure reflected by the nuclear distribution. We have also found that interaction energy of NH₃H⁺···DBeH is stronger than that of NH₃D⁺···HBeH and isotopic deshielding effect of magnetic shielding becomes large in lighter isotope. © 2013 Wiley Periodicals, Inc.     

Effect of Al?H···H?O dihydrogen bond on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex. An ONIOM DFT/AM1 study

To elucidate the nature of the Al? H···H? O dihydrogen bond and its effect on the reaction between diphenylmethanol and pyrazolate‐bridged dialuminum complex, a theoretical study was carried out using the ONIOM(B3LYP/6‐31+G(d,p):AM1) method. Calculations indicate that this reaction is a two‐step process. The first step is nucleophilic addition and the resulting intermediate is stabilized by an Al? H···H? O dihydrogen bond. Topology analyses based on the “atoms‐in‐molecules” theory show that the Al? H···H? O dihydrogen bond in dialuminum intermediate is stronger than normal hydrogen bond. This step is not barrierless, which is contrary to the result predicted by using simplified model. The second step, eliminating a molecule of dihydrogen, requires an activation free energy of 9.9 kcal/mol in gas phase, which implies the simplified model underestimates the energy barrier of this elimination step. ONIOM calculations also show that, using the simplified model without zero‐point energy correction, the dihydrogen bonding strength has been underestimated and unreliable results have been obtained. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Concerted Interaction between Pnicogen and Halogen Bonds in XCl?FH2P?NH3 (X=F,OH, CN,NC, and FCC)

We analyze the interplay between pnicogen‐bonding and halogen‐bonding interactions in the XCl? FH₂P? NH₃ (X=F, OH, CN, NC, and FCC) complex at the MP2/aug‐cc‐pVTZ level. Synergetic effects are observed when pnicogen and halogen bonds coexist in the same complex. These effects are studied in terms of geometric and energetic features of the complexes. Natural bond orbital theory and Bader’s theory of “atoms in molecules” are used to characterize the interactions and analyze their enhancement with varying electron density at critical points and orbital interactions. The physical nature of the interactions and the mechanism of the synergetic effects are studied using symmetry‐adapted perturbation theory. By taking advantage of all the aforementioned computational methods, the present study examines how both interactions mutually influence each other.     

Cooperative influence of water binding to peptides by N?H···OH2 and CO···HOH hydrogen bonds: Study by Ab Initio calculations

In this article, the geometry structures of hydrogen bond chains of formamide and N‐methylacetamide and their hydrogen‐bonded complexes with water were optimized at the MP2/6‐31G* level. Then, we performed Møller–Plesset perturbation method with 6‐311++g**, aug‐cc‐pvtz basis sets to study the cooperative influence to the total hydrogen bond energy by the N? H ··· OH₂ and C?O ··· HOH hydrogen bonds. On the basis of our results, we found that the cooperativity of the hydrogen‐bonded complexes become weaker as N? H ··· OH₂ and C?O ··· HOH hydrogen bonds replacing N? H ··· O?C hydrogen bonds in protein and peptide. It means that the N? H and C?O bonds in peptide prefer to form N? H ··· O?C hydrogen bond rather than to form C?O ··· HOH and N? H ··· OH₂. It is significant for understanding the structures and properties of the helical or sheet structures of protein and peptide in biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

An ab initio interpretation in gas phase and aqueous solution of the generalized anomeric effect in R?O?CR2?NR2 (R = H,CH3)

The conformational stability of aminomethanol and its methylated derivatives has been investigated by means of ab initio methods in the gas phase and aqueous solution. Among the computational levels employed, HF/6‐31G**//HF/6‐31G** calculations correctly describe the conformational features of this series of compounds, and agree well with the results obtained using larger basis sets and including ZPE or electron correlation corrections. Calculated energies and geometries follow the known trends associated to the generalized anomeric effect. Thus, the most stable conformers exhibit preferences for the trans orientations of the Lp N C O and Lp O C N moieties. However, reverse anomeric effects are observed when a methyl group is bonded to the oxygen, because the Lp O C N unit prefers a gauche orientation (that is, trans Me O C N). The natural bond orbital (NBO) method was employed to explain the cited conformational preferences. According to the NBO results, trans arrangements are preferred because the stabilization due to charge delocalization is more important than electrostatic and steric contributions. This explanation agrees with the conclusions obtained by other independent procedures based on energy decomposition schemes. The NBO method was also used to explain the origin of the rotational barriers around the C O and C N bonds in terms of the balance between unfavorable hyperconjugation and electrostatic and steric effects. Changes in conformational stability caused by methylations in different molecular positions were also explained by the influence of the methyl groups on lone‐pair delocalization and on steric effects. Finally, the effect of solvation was studied by means of the ab initio PCM method, and the significant changes on relative energies found were analyzed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 462–477, 2000     

Catalytic C?C,C?N,and C?O Ullmann‐Type Coupling Reactions

Copper‐catalyzed Ullmann condensations are key reactions for the formation of carbon–heteroatom and carbon–carbon bonds in organic synthesis. These reactions can lead to structural moieties that are prevalent in building blocks of active molecules in the life sciences and in many material precursors. An increasing number of publications have appeared concerning Ullmann‐type intermolecular reactions for the coupling of aryl and vinyl halides with N, O, and C nucleophiles, and this Minireview highlights recent and major developments in this topic since 2004.     

M4(CH2)4 Cubane‐Type Rare‐Earth Methylidene Complexes: Unique Reactivity toward Unsaturated C?O,C?N,and C?S Bonds

The reactivity of the cubane‐type rare‐earth methylidene complex [Cp′Lu(μ₃‐CH₂)]₄ ( 1 , Cp′=C₅Me₄SiMe₃) with various unsaturated electrophiles was investigated. The reaction of 1 with CO (1 atm) at room temperature gave the bis(ketene dianion)/dimethylidene complex [Cp′₄Lu₄(μ₃‐CH₂)₂(μ₃,η²‐O‐C?CH₂)₂] ( 2 ) in 86 % yield through the insertion of two molecules of CO into two of the four lutetium–methylidene units. In the reaction with the sterically demanding N,N‐diisopropylcarbodiimide at 60 °C, only one of the four methylidene units in 1 reacted with one molecule of the carbodiimide substrate to give the mono(ethylene diamido)/trimethylidene complex [Cp′₄Lu₄(μ₃‐CH₂)₃{iPrNC(=CH₂)NiPr}] ( 3 ) in 83 % yield. Similarly, the reaction of 1 with phenyl isothiocyanate gave the ethylene amido thiolate/trimethylidene complex [Cp′₄Lu₄(μ₃‐CH₂)₃{PhNC(S)=CH₂}] ( 4 ). In the case of phenyl isocyanate, two of the four methylidene units in 1 reacted with four molecules of the substrate at ambient temperature to give the malonodiimidate/dimethylidene complex [Cp′₄Lu₄(μ₃‐CH₂)₂{PhN=C(O)CH₂(O)C?NPh}₂] ( 5 ) in 87 % yield. In this reaction, each of the two lutetium–methylidene bonds per methylidene unit inserted one molecule of phenyl isocyanate. All the products have been fully characterized by NMR spectroscopy, X‐ray diffraction, and microelemental analyses.     

An insight into C?H···N hydrogen bond and stability of the complexes formed by trihalomethanes with ammonia and its monohalogenated derivatives

A theoretical study of the C? H···N hydrogen bond in the interactions of trihalomethanes CHX₃ (X = F, Cl, Br) with ammonia and its halogen derivatives NH₂Y (Y = F, Cl, Br) has been carried out thoroughly. The complexes are quite stable, and their stability increases in going from CHF₃ to CHCl₃ then to CHBr₃ when Y keeps unchanged. With the same CHX₃ proton donor, enhancement of the gas phase basicity of NH₂Y strengthens stability of the CHX₃···NH₂Y complex. The C? H···N hydrogen bond strength is directly proportional to the increase of proton affinity (PA) at N site of NH₂Y and the decrease of deprotonation enthalpy (DPE) of C? H bond in CHX₃. The CHF₃ primarily appears to favor blue shift while the red‐shift is referred to the CHBr₃. The blue‐ or red‐shift of CHCl₃ strongly depends on PA at N site of NH₂Y. We suggest the ratio of DPE/PA as a factor to predict which type of hydrogen bond is observed upon complexation. The SAPT2+ results show that all C? H···N interactions in the complexes are electrostatically driven regardless of the type of hydrogen bond, between 48% and 61% of the total attractive energy, and partly contributed by both induction and dispersion energies.     

Singlet methylene insertion into polar O?H and N?H bonds of water and ammonia—Ab initio and DFT study

Correlated ab initio molecular orbital, DFT, QCISD, G3MP2, and QCISD(T) calculations have been used to investigate the geometries, energetics, and mechanisms governing the insertion reactions of ¹CH₂ into O H and N H bonds of water and ammonia, respectively, in gas phase adopting 6‐311++g(d, p) basis set. It is found that ¹CH₂ reacts with water and ammonia to produce the ylide‐like intermediates H₂C OH₂ and H₂C NH₃, which in turn undergo 1,2‐hydrogen shift to produce methanol and methylamine, respectively. Results obtained indicate that in the gas phase, the ylides and the transition states are located below the reactants' energy levels. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Modeling the H bond donor strength of ?OH, ?NH,and ?CH sites by local molecular parameters

A quantum chemical model is introduced to predict the H‐bond donor strength of monofunctional organic compounds from their ground‐state electronic properties. The model covers ? OH, ? NH, and ? CH as H‐bond donor sites and was calibrated with experimental values for the Abraham H‐bond donor strength parameter A using the ab initio and density functional theory levels HF/6‐31G** and B3LYP/6‐31G**. Starting with the Morokuma analysis of hydrogen bonding, the electrostatic (ES), polarizability (PL), and charge transfer (CT) components were quantified employing local molecular parameters. With hydrogen net atomic charges calculated from both natural population analysis and the ES potential scheme, the ES term turned out to provide only marginal contributions to the Abraham parameter A, except for weak hydrogen bonds associated with acidic ? CH sites. Accordingly, A is governed by PL and CT contributions. The PL component was characterized through a new measure of the local molecular hardness at hydrogen, η(H), which in turn was quantified through empirically defined site‐specific effective donor and acceptor energies, EE_occ and EE_vac. The latter parameter was also used to address the CT contribution to A. With an initial training set of 77 compounds, HF/6‐31G** yielded a squared correlation coefficient, r², of 0.91. Essentially identical statistics were achieved for a separate test set of 429 compounds and for the recalibrated model when using all 506 compounds. B3LYP/6‐31G** yielded slightly inferior statistics. The discussion includes subset statistics for compounds containing ? OH, ? NH, and active ? CH sites and a nonlinear model extension with slightly improved statistics (r² = 0.92). © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Rhodium(I)‐Catalyzed Sequential C(sp)?C(sp3) and C(sp3)?C(sp3) Bond Formation through Migratory Carbene Insertion

A Rh^I‐catalyzed three‐component reaction of tert‐propargyl alcohol, diazoester, and alkyl halide has been developed. This reaction can be considered as a carbene‐involving sequential alkyl and alkynyl coupling, in which C(sp) C(sp³) and C(sp³) C(sp³) bonds are built successively on the carbenic carbon atom. The Rh^I‐carbene migratory insertion of an alkynyl moiety and subsequent alkylation are proposed to account for the two separate C C bond formations. This reaction provides an efficient and tunable method for the construction of all‐carbon quaternary center.