The interplay between charge transfer,rehybridization, and atomic charges in the internal geometry of subunits in noncovalent interactions

When a noncovalent bond is formed, there is frequently some charge transfer from one subunit to the other. The interaction also causes changes in the atomic charges and hybridization patterns of bonding orbitals. The manner in which these various effects combine to cause elongations or contractions of bonds within the individual subunits is examined. In both the cases of CH···O H‐bonds and P···N pnicogen bonds, the bond length changes are consistent with the guiding principles generally known as Bent's rules. © 2014 Wiley Periodicals, Inc.     

A theoretical study of the dihydrogen molecule confined inside carbon nanotubes

The aim of this work is to better understand the interaction between the confined dihydrogen molecule and armchair (2,2), (3,3) (4,4), (5,5), and (6,6) single‐walled carbon nanotubes (SWNT) using Restricted Hartree–Fock (RHF) and Density Functional Theory (DFT) methods using B3LYP and CAM‐B3LYP functionals. Depending on the calculation method and its orientation inside the nanotube, H₂ binds differently. We found that H? H bond length increases when H₂ is trapped in CNT (2,2) and decreases for CNT (3,3) and (4,4). The characteristics of confined H₂ in (5,5) and (6,6) nanotubes are similar to H₂ in a free state. © 2013 Wiley Periodicals, Inc.     

Influence of substitution on the strength and nature of CH···N hydrogen bond in XCCH···NH3 complexes

The effect of substitution on the strength and nature of CH···N hydrogen bond in XCCH···NH₃ (X = F, Cl, Br, OH, H, Me) and NCH···NH₃ complexes were investigated by quantum chemical calculations. Ab initio calculations were performed using MP2 method with a wide range of basis sets. With tacking into account the BSSE and ZPVE, the values of BEs decrease. Replacement of the nonparticipatory hydrogen atom of HCCH by the electronegative atoms (F, Cl, and Br), lead to the BEs increases. The BE corresponding to the replacement of the nonparticipatory hydrogen atom of HCCH by the OH and CH₃ groups decreases. A far greater enhancement of the interaction energy arises from replacement of HCCH by the more acidic HCN. The natural bond orbital analysis and the Bader's quantum theory of atoms in molecules were also used to elucidate the interaction characteristics of these complexes. The electrostatic nature of H‐bond interactions is predicted from QTAIM analysis. In addition, the relationship between the isotropic and anisotropic chemical shifts of the bridging hydrogen and binding energy of complexes as well as electron density at N···H BCPs were investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

亚烷基锡烯与乙烯环加成反应机理的理论研究

The mechanism of a cycloaddition reaction between singlet alkylidenestannylene and ethylene has been investigated with MP2/3-21 G^* and B3LYP/3-21 G* methods, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. Energies for the involved conformations were calculated by CCSD(T)//MP2/3-2 IG^* and CCSD(T)//B3LYP/3-21G^* methods, respectively. The results show that the dominant reaction pathway of the cycloaddition is that an intermediate (INT) is firstly formed between the two reactants through a barrier-free exothermic reaction of 39.7 kJ/mol, and the intermediate then isomerizes to a four-membered ring product (P2.1) via a transition state TS2.1 with a barrier of 66.8 kJ/mol.     

Theoretical investigation on identical anionic halide‐exchange SN2 reaction processes on N‐haloammonium cation NH3X+ (X = F,Cl, Br,and I)

CCSD(T) calculations have been used for identically nucleophilic substitution reactions on N‐haloammonium cation, X^? + NH₃X⁺ (X = F, Cl, Br, and I), with comparison of classic anionic S_N2 reactions, X^? + CH₃X. The described S_N2 reactions are characterized to a double curve potential, and separated charged reactants proceed to form transition state through a stronger complexation and a charge neutralization process. For title reactions X^? + NH₃X⁺, charge distributions, geometries, energy barriers, and their correlations have been investigated. Central barriers ΔE for X^? + NH₃X⁺ are found to be lower and lie within a relatively narrow range, decreasing in the following order: Cl (21.1 kJ/mol) > F (19.7 kJ/mol) > Br (10.9 kJ/mol) > I (9.1 kJ/mol). The overall barriers ΔE relative to the reactants are negative for all halogens: ?626.0 kJ/mol (F), ?494.1 kJ/mol (Cl), ?484.9 kJ/mol (Br), and ?458.5 kJ/mol (I). Stability energies of the ion–ion complexes ΔE_comp decrease in the order F (645.6 kJ/mol) > Cl (515.2 kJ/mol) > Br (495.8 kJ/mol) > I (467.6 kJ/mol), and are found to correlate well with halogen Mulliken electronegativities (R² = 0.972) and proton affinity of halogen anions X^? (R² = 0.996). Based on polarizable continuum model, solvent effects have investigated, which indicates solvents, especially polar and protic solvents lower the complexation energy dramatically, due to dually solvated reactant ions, and even character of double well potential in reactions X^? + CH₃X has disappeared. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Synthesis,Spectroscopy and Crystal Structures of Chiral Organic Ammonium Tetrathiometalates Showing N‐H···S and C‐H···S Interactions

The reaction of ammonium tetrathiometalate (NH₄)₂[MS₄] (M = W or Mo) with the R(+) or S(?) forms of the organic amine α‐methylbenzylamine [PhCH(CH₃)NH₂] results in the formation of the corresponding non‐centrosymmetric bis(α‐methylbenzylammonium) tetrathiometalate complexes [PhCH(CH₃)NH₃]₂[MS₄] (R‐ammonium M = W 1 ; R‐ammonium M = Mo 2 ; S‐ammonium M = W 3 , S‐ammonium M = Mo 4 ) which were characterized by elemental analysis, IR, Raman, UV‐Vis and CD spectra, X‐ray powder diffractometry and single crystal X‐ray crystallography. Compounds 1 ‐ 4 crystallize in the chiral space group P2₁ and constitute the first examples of structurally characterized chiral organic ammonium group VI tetrathiometalates. The structures of 1 ‐ 4 consist of two crystallographically independent chiral organic ammonium cations and a tetrahedral tetrathiometalate dianion. The N‐H···S and C‐H···S interactions between the anions and cations organise them such that the organic ammonium ions always point towards the S atoms of [MS₄]^2?.     

SiC2S分子结构和光谱的理论研究

在CCSD（T）/6-311G（2df)//B3LYP/6-311G(d)水平上对SiC2S的各种可能异构体进行了研究。得到了其几何构型,精确能量和红外光谱。结果表明：SiC2S有8个稳定的异构体,能量最低的是直线型,电子态为^1∑的SiCCP1,其次是C2v对称性的S-cSiCC5,第三稳定的是直线型^1∑电子态异构体SSiCC2,第四稳定的是具有CC桥键C2v对称性的长菱形结构的.     

Mechanism and kinetics of the reaction of the 2-propargyl radical with ammonia

Gas-phase mechanism and kinetics of the reactions of the 2-propargyl radical (H₂CCCH), an important intermediate in combustion processes, with ammonia were investigated using ab initio molecular orbital theory at the coupled-cluster CCSD(T)//B3LYP/6-311++G(3df,2p) method in conjunction with transition state theory (TST), variational transition state theory (VTST), and Rice–Ramsperger–Kassel–Macus (RRKM) calculations for rate constants. The potential energy surface (PES) constructed shows that the C₃H₃ + NH₃ reaction has four main entrances, including two H-abstraction and two addition channels in which the former are energetically more favorable. The H-abstraction channels occur via energy barriers of 24 (T0/P2) and 26 kcal/mol (T0/P3) forming loose van de Waals complexes, COM_1 (12 kcal/mol) and COM_2 (14 kcal/mol), respectively. These complexes can easily be decomposed via barrier-less processes resulting HCCCH₃ + NH₂ (P2, 14 kcal/mol) and HCCCH₃ + NH₂ (P3, 15 kcal/mol), respectively. The additional channels occur initially by formation of two intermediate states, H₂CCCHNH₃ (35 kcal/mol) and H₂CC(NH₃)CH (37 kcal/mol) via energy barriers of 37 and 40 kcal/mol at T0/1 and T0/5, respectively, followed by isomerization and decomposition yielding 21 different products. These processes are fully depicted in an as-complete-as-possible PES. The rate constants and product branching ratios for the low-energy channels calculated show that the C₃H₃ + NH₃ reaction is almost pressure-independent. For the temperature range of 300–2000 K, the HCCCH₃ + NH₂ is the major product, whereas the minor one, HCCCH₃ + NH₂, has more contribution when temperature increases. Theoretical results on the mechanism and kinetics of the reaction considered may be helpful for future experiments as well as for understanding the role of the propargyl radical in combustion chemistry.     

Insight into the π‐hole···π‐electrons tetrel bonds between F2ZO (Z = C,Si, Ge) and unsaturated hydrocarbons

The intermolecular π‐hole···π‐electrons interactions between F₂ZO (Z = C, Si, Ge) molecules and unsaturated hydrocarbons including acetylene, ethylene, 1,3‐butadiene and benzene were constructed to reveal the differences of tetrel bonds forming by carbon and heavier tetrel atoms. The ab initio computation in association with topological analysis of electron density, natural bond orbital, and energy decomposition analysis demonstrate that the strength of Si···π and Ge···π tetrel bonds is much stronger than that of C···π tetrel bonds. The Si···π and Ge···π tetrel bonds exhibit covalent or partially covalent interaction nature, while the weak C···π tetrel bonds display the hallmarks of noncovalent interaction, the electrostatic interaction is the primary influencing factor. The Si···π and Ge···π interactions are determined by both the σ‐ and π‐electron densities, while the C···π interactions are dominated mainly by the π‐electron densities. The π‐hole···π‐electrons tetrel bonds are dominated by electrostatic interaction, and polarization has a comparable contribution in the Si···π and Ge···π tetrel bonds.     

A dataset of highly accurate homolytic NBr bond dissociation energies obtained by Means of W2 theory

Homolytic N? Br bond dissociation constitutes the initial step of numerous reactions involving N‐brominated species. However, little is known about the strength of N? Br bonds toward homolytic cleavage. We herein report accurate bond dissociation energies (BDEs) for a set of 18 molecules using the high‐level W2 thermochemical protocol. The BDEs (at 298 K) of the species in this set range from 162.2 kJ mol^?1 (N‐bromopyrrole) to 260.6 kJ mol^?1 ((CHO)₂NBr). In order to compute BDEs of larger systems, for which W2 theory is not applicable, we have benchmarked a wide range of more economical theoretical procedures. Of these, G3‐B3 offers the best performance (root‐mean‐square deviations = 2.9 kJ mol^?1), and using this method, we have computed N? Br BDEs for four widely used N‐brominated compounds. These include (BDEs are given in parentheses): N‐bromosuccinimide (281.6), N‐bromoglutarimide (263.2), N‐bromophthalimide (274.7), and 1,3‐dibromo‐5,5‐dimethylhydantoin (218.2 and 264.8 kJ mol^?1). © 2015 Wiley Periodicals, Inc.     

C—H···X (X = N,O, S) intramolecular interaction in 1‐vinyl‐2‐(2′‐heteroaryl)pyrroles as monitored by 1H and 13C NMR spectroscopy

¹H and ¹³C NMR spectroscopy of a series of 1‐vinyl‐2‐(2′‐heteroaryl)‐pyrroles were employed for the analysis of their electronic and spatial structure. The C—H···N intramolecular interaction between the α‐hydrogen of the vinyl group and the pyridine nitrogen, a kind of hydrogen bonding, was detected in 1‐vinyl‐2‐(2′‐pyridyl)pyrrole, which disappeared in its iodide methyl derivative. It was shown that this interaction is stronger than the C—H···O and C—H···S interactions in 1‐vinyl‐2‐(2′‐furyl)‐ and ‐2‐(2′‐thienyl)‐pyrroles. Copyright © 2001 John Wiley & Sons, Ltd.     

The Balance between Hydrogen Bonds,Halogen Bonds,and Chalcogen Bonds in the Crystal Structures of a Series of 1,3,4-Chalcogenadiazoles

In order to explore how specific atom-to-atom replacements change the electrostatic potentials on 1,3,4-chalcogenadiazole derivatives, and to deliberately alter the balance between intermolecular interactions, four target molecules were synthesized and characterized. DFT calculations indicated that the atom-to-atom substitution of Br with I, and S with Se enhanced the σ-hole potentials, thus increasing the structure directing ability of halogen bonds and chalcogen bonds as compared to intermolecular hydrogen bonding. The delicate balance between these intermolecular forces was further underlined by the formation of two polymorphs of 5-(4-iodophenyl)-1,3,4-thiadiazol-2-amine; Form I displayed all three interactions while Form II only showed hydrogen and chalcogen bonding. The results emphasize that the deliberate alterations of the electrostatic potential on polarizable atoms can cause specific and deliberate changes to the main synthons and subsequent assemblies in the structures of this family of compounds.     

Revisiting the reactivity of different carbon bases: A theoretical study

Quantum chemical calculations are performed on different carbon bases to understand the origin of their reactivity. Both carbon(0) and carbon(II) bases may show very high values of second proton affinity as well as bond dissociation energies for gem‐dimetallation. Thus, their distinction becomes blurred when subjected to electrophilic attack. However, unlike carbon(0) bases, carbon(II) bases are ambiphilic in nature owing to the presence of a σ symmetric lone pair and a vacant π orbital concentrated on the central carbon atom. Thus, they may show different reactivity when subjected to nucleophilic attack. This reactivity difference may be considered as another distinction between these two classes of compounds. © 2013 Wiley Periodicals, Inc.     

A theoretical investigation of the mechanism for the reaction between a quebrachitol derivative and N3−

The reaction between a mesylated compound and sodium azide was previously studied experimentally at a temperature of 140 °C using dimethylformamide as a solvent. The product was assigned on the basis of the analysis of the NMR spectra. In this work semiempirical (AM1 and PM3), ab initio (Hartree–Fock and MP2) and density functional theory (BLYP functional) quantum mechanical calculations, using continuum models for describing the solvent effect, were carried out for this process to better understand the reaction mechanism. Three distinct mechanisms involving a carbocation and epoxide intermediates, and a transition-state structure for direct attack of the N₃ ⁻ species to the reactant were investigated. The theoretically calculated preferred reaction pathway passing through an epoxide intermediate agrees nicely with the experimental proposal, providing a good example of where theoretical calculations can be of great help to definitively elucidate the reaction mechanism. Received: 10 July 2001 / Accepted: 20 December 2001 / Published online: 8 April 2002     

Synthesis and Characterization of (–)‐Menthyl Containing N‐Alkyl Cycloimmonium Salts

The reaction of 4‐phenyl‐2‐aminothiazole or 2‐amino pyridine with α‐bromo acetic (–)‐menthyl ester ( 2c ) yields new N‐alkyl cycloimmonium bromides ( 1c , 3 ) with the chiral (–)‐menthyl substituent, which were isolated and fully characterized by ¹H and ¹³C NMR spectroscopy for the first time. In addition, starting from 4‐phenyl‐2‐aminothiazole, two further N‐alkyl cycloimmonium bromides ( 1a , 1b ) were prepared. The molecular and crystal structures of all three thiazole derived N‐alkyl cycloimmonium bromides ( 1a – c ) were determined by single‐crystal X‐ray diffraction. In all cases the crystal structures are dominated by N–H ··· Br hydrogen bonds, which results in the formation of an extensive hydrogen bonded network in the crystal. Interestingly, in all structures S ··· Br^– distances shorter than the sum of the van der Waals radii are observed.     

钠与惰性气体及烷烃准分子对吸收系数的实验与理论评价

准分子泵浦钠金属激光器(XPNaL)在钠导星中有着极为重要的应用。但是,传统的准分子对,例如Na-He和Na-Ar等对相对于泵浦源的吸收系数很小。本文对Na-Ar、Na-Xe、Na-CH₄、Na-C₂H₆四个体系进行了研究,从荧光实验和结合能的高精度量化理论计算两方面来探究比较好的准分子对。实验结果表明:这四个准分子对体系的荧光强度曲线峰面积比为1.0 : 6.4 : 4.9 : 10.4。同时,通过CCSD(T)手段和基组外推法对Na-Ar、Na-Xe、Na-CH₄和Na-C₂H₆准分子对的结合能计算结果分别为52.8、124.5、117.7和150.0cm^-1。因此,可以推断量化计算与实验结果能够较好地符合。随后, Na-C₂H₆准分子对从实验和理论两方面被发现是效率最高的体系,更有希望被发展成为高能准分子宽带泵浦钠金属激光器。本工作还证明了采用大基组对结合能的高精度量化计算,对用于准分子宽带泵浦碱金属激光器的准分子对筛选是很好的评判标准。     

A computational investigation of the sulphuric acid‐catalysed 1,4‐hydrogen transfer in higher Criegee intermediates

Criegee intermediates (CIs) are formed during the ozonolysis of unsaturated hydrocarbons in the troposphere. The fate of CIs is of critical importance to tropospheric oxidation chemistry, particularly in the context of radical and secondary organic aerosol formation. Using the high‐level ab initio G4(MP2) method, we investigate the 1,4 hydrogen shift reaction in CIs formed from ozonolysis of two common biogenic hydrocarbons: isoprene and α‐pinene. We consider the uncatalysed reaction, as well as the reaction catalysed by a water molecule and by sulphuric acid. We show that sulphuric acid is a very effective catalyst, leading to a barrierless tautomerization relative to the free reactants and to very low reaction barrier heights relative to the reactant complexes. In particular, we obtain reaction barrier heights of Δ = 24.5 (isoprene CI) and 8.4 (α‐pinene CI) kJ mol⁻¹ relative to the reactant complexes. Given the reaction of OH radicals with SO₂ in the troposphere can ultimately yield sulphuric acid, these findings may have significant consequences for current atmospheric chemical models for regions of high sulphur concentrations.     

Is the DPT tautomerization of the long A·G Watson–Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question

Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum‐mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ? A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H‐bonds) and the N2H···HC2 dihydrogen bond (DH‐bond) (0.68 kcal·mol^?1), whereas the A*·G* base mispair—by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H‐bonds (0.42 kcal·mol^?1). The N2H···HC2 DH‐bond smoothly and without bifurcation transforms into the C2H···N2 H‐bond at the IRC = ?10.07 Bohr in the course of the A·G ? A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H‐bonds, it was observed that the N6H···O6 H‐bond is anticooperative to the two others—N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H‐bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10^?14 s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low‐frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be considered as a source of the mutagenic tautomers of the DNA bases, as the A·G base mispair dissociates during DNA replication exceptionally into the A and G monomers in the canonical tautomeric form. © 2013 Wiley Periodicals, Inc.     

Influence of the C—H· · ·N intramolecular interaction on the spatial structures and 1H and 13C NMR parameters of heteroaryl vinyl ethers and sulfides

A complete analysis of the ¹H and ¹³C spectra of the representative series of heteroaryl vinyl ethers and sulfides and heteroaryl styryl sulfides was carried out. The electronic and spatial structures of these compounds are discussed. It was shown that the C—H· · ·N intramolecular interactions in the investigated molecules influence significantly the spectral parameters and the conformational equilibrium. Copyright © 2003 John Wiley & Sons, Ltd.     

HS和HONO反应机理的研究

采用密度泛函和耦合簇理论方法研究了HS与HONO的反应机理.在B3LYP/6-311+G(2df,2p)水平上对HS+HONO反应中的所有物种进行了几何构型优化和频率分析,通过内禀反应坐标(IRC)确认了反应物、过渡态、中间体和产物之间的相关性;采用CCSD(T)/6-311+G(2df,2p)方法获得了各物种的单点能.计算结果表明:HS+HONO的主要反应通道为HS+cis-HONO→p2-cis-IM1→p2-cis-TS→p2-IM2→P2(H_2S+NO_2),其反应活化能为71.26kJ·mol~(-1).