Interplay of noncovalent interactions in antiseptic quaternary ammonium surfactant Miramistin

The molecular and crystal structure of the widely used antiseptic benzyldimethyl{3‐[(1‐oxotetradecyl)amino]propyl}ammonium chloride monohydrate (Miramistin, MR ), C₂₆H₄₇N₂O⁺·Cl^?·H₂O, was determined by a single‐crystal X‐ray diffraction study and analyzed in the framework of the QTAIM (quantum theory of atoms in molecules) approach using both periodic and molecular DFT (density functional theory) calculations. The various noncovalent intermolecular interactions of different strengths were found to be realized in the hydrophilic parts of the crystal packing (i.e. O—H…Cl, N—H…Cl, C—H…Cl, C—H…O and C—H…π). The hydrophobic parts are built up exclusively by van der Waals H…H contacts. Quantification of the interaction energies using calculated electron‐density distribution revealed that the total energy of the contacts within the hydrophilic and hydrophobic regions are comparable in value. The organic MR cation adopts the bent conformation with the head group tilted back to the long‐chain alkyl tail in both the crystalline and the isolated state due to stabilization of this geometry by several intramolecular C—H…π, C—H…N and H…H interactions. This conformation preference is hypothesized to play an important role in the interaction of MR with biomembranes.     

Phosphoramides: Synthesis,Spectroscopy, and X‐ray Crystallography

A series of new phosphoramides with general formula RP(O)X₂, where R = amino/p‐methylphenoxy and X = amine, were synthesized and characterized by ¹H, ¹³C, ³¹P nuclear magnetic resonance (NMR), and infrared (IR) spectroscopy and elemental analysis. The ³¹P{¹H} NMR spectra show that among compounds 7–9 containing 2‐, 3‐, and 4‐aminopyridinyl moieties, respectively, the shielding order of the P atom decreases as 7 > 9 > 8 . Also, the structure of compound 7 was determined by X‐ray crystallography. In this structure, repeated noncentrosymmetric dimers are formed by two strong intermolecular N(1)‐H(1N)…N(2) and N(3)‐H(3N)…O(1) hydrogen bonds. Taking into account weak intermolecular C(17)‐H(17C)…N(4), C(17)‐H(17E)…N(4), C(2)‐H(2A)…O(2), and also weak aromatic C—H…C interactions, a three‐dimensional polymeric chain is created in the crystalline network. The density functional theory calculations at B3LYP, B3PW91, and M06 levels using the 6–31+G** basis set were in good agreement with the X‐ray crystallography data.     

Interactions of Anionic and Neutral Serine with Pure and Metal-doped Graphene Studied by Density Functional Theory

We present a theoretical study of interactions of anionic and neutral serine (Ser) on pure or metal-doped graphene surfaces using density functional theory calculations. Interactions of both types of Ser with the pure graphene surface show weak non-covalent interactions due to the formation of -COOH…π, -COO^-…π, and -OH…π interactions. On metaldoped graphene, covalent interactions to the surface dominate, due to the formation of strong metal-O and O-metal-O interactions. Furthermore, the doped Fe, Cr, Mn, Al, or Ti enhances the ability of graphene to attract both types of Ser by a combination of the adsorption energy, the density of states, the Mulliken atomic charges, and differences of electron density. At the same time, the interaction strengths of anionic Ser on various graphene surfaces are stronger than those of neutral Ser. These results provide useful insights for the rational design and development of graphene-based sensors for the two forms of Ser by introducing appropriate doped atoms. Ti and Fe are suggested to be the best choices among all doped atoms for the anionic Ser and neutral Ser, respectively.     

OCS,CO2,N2O与烯、炔烃之间π…π作用的电子密度拓扑研究

采用MP2/aug-cc-pVDZ方法对氧硫化碳(OCS)、二氧化碳(CO2)、一氧化二氮(N2O)与乙烯(C2H4)、乙炔(C2H2)、2-丁炔(C4H6)之间形成的平行构型复合物中的分子间相互作用进行了理论研究.复合物的相互作用能按照B…C2H4B…C2H2>B…C4H6(B=OCS,CO2,N2O)的顺序依次减小.采用电子密度拓扑分析理论方法,讨论了复合物中π…π作用的成键特性.电子密度拓扑分析表明复合物中形成了弱的分子间相互作用,且以静电作用为主;π电子密度分子图与全电子密度分子图中键径方向是一致的,说明π…π作用在本文所讨论的体系中起着很重要的作用.NBO分析表明净电荷迁移从电子给体C2H4,C2H2,C4H6到电子受体OCS,CO2,N2O,迁移数按照B…C2H4相似文献   

Synthesis and Crystal Structure of N-(1,3,4-Thiadiazol-2-yl)-1-[1-(6-chloropyridin-3-yl)methy]-5-methyl-1H-[1,2,3]triazol-4-carboxamide

The crystal structure of the title compound (C12H10ClN7OS,Mr=335.78) has been determined by single-crystal X-ray diffraction. The crystal is of triclinic,space group P1 with a=8.4093(11),b=9.4430(12),c=11.1454(14),α=95.508(2),β=111.366(2),γ=115.259(2)°,V=711.42(16) 3,Z=2,Dc=1.568 g/cm3,F(000)=344,μ(MoKα)=0.428 mm-1,the final R=0.0476 and wR=0.1243 for 2353 observed reflections (I > 2σ(I)). The dihedral angles between the pyridine and triazole,thiazole and triazole,and pyridine and thiazole rings are 69.2(1),9.2(1) and 72.7(1)o,respectively. Intramolecular C(8)-H(8B)…O(1) and N(5)-H(5A)…N(4) as well as intermolecular C(5)-H(5)…S(1),C(3)-H(3)…N(6) and N(5)-H(5A)…N(1) hydrogen bonds together with weak C-H…π hydrogen-bonding and π-π stacking interactions contribute to the stability of the structure. There is also evidence for significant electron delocalization in the triazolyl system.     

Supramolecular architecture of crystals of perfluorinated 3-alkylphthalides

The molecular and crystal structures of perfluoro-3-alkylphthalides (3-hydroxyperfluoro-3-methylphthalide and its hydrate, two polymorphs of 3-hydroxyperfluoro-3-ethylphthalide and 3-hydroxyperfluoro-3-isopropylphthalide) are determined by single crystal X-ray diffraction. In the crystals, the supramolecular O–Н…O=C synthon occurs leading, except the crystallohydrate, to the formation of C₁¹ (6) hydrogen bonded chains (supramolecular 1D motifs). According to the DFT/M06-2X/TZV calculations, the interaction energy of hydrogen bonded molecular pairs increases in this series, which can be explained by additional C=O…π, O…π, and C–F…π interactions.     

双齿甜菜碱衍生物大环及双环镉(Ⅱ)配位化合物的合成与晶体结构

利用甜菜碱衍生物1,5-二(4-羧基吡啶基)-N-甲基二乙胺(L)合成了两种镉(Ⅱ)的配位化合物[Cd2Cl4(H2O)2L2].2H2O和[Cd2(SCN)4(μ-H2O)L2]。用X-射线单晶衍射仪测定了配合物的单晶结构,并对它们进行了元素分析、红外光谱、1H NMR、热重等表征。结构分析表明,前者具有三十六元大环框架,而后者为双环结构。由于缺乏分子之间的强烈相互作用,弱相互作用决定了这两种化合物在晶格中的堆积模式:前者由相邻分子间的π-π和C-H…π相互作用而堆积形成二维砖墙的结构;后者由配位的SCN-阴离子通过S…S弱相互作用联接成一维链状结构。     

Synthesis and Crystal Structure of One New Adduct of Isonicotinamide and 3,5-Dinitrosalicylic Acid

One new organic adduct,isonicotinamide·3,5-dinitrosalicylic acid with isonico-tin-amide(ina) and 3,5-dinitrosalicylic acid(3,5-dnsa) in 1:1 molar ratio,has been synthesized.Its struc-ture(C13H10N4O8,Mr = 350.25) was characterized by elemental analysis,IR and single-crystal X-ray diffraction analysis.The crystal belongs to the triclinic system,space group P1,with a = 8.812(4),b = 9.487(5),c = 9.604(6) ,α = 116.54(2),β = 97.29(5),γ = 98.35(4)°,V = 693.8(7) 3,Z = 2,Dc = 1.677 g/cm3,λ(MoKα) = 0.71073 ,μ = 0.142 mm-1,F(000) = 360,the final R = 0.0539 and wR = 0.1402 for 2417 unique reflections(Rint = 0.0288) with 1819 observed ones(Ⅰ 2σ(Ⅰ)).Proton transfer reaction occurs between 3,5-dnsa and ina molecules,and the hydrogen bonds(N-H…O and C-H…O) with other interactions(π…π stacking and weak interactions of O…O and C…O) cooperatively construct a three-dimensional(3D) supramolecular structure.     

Unraveling weak interactions in aniline-pyrrole dimer clusters

Weak intermolecular interactions in aniline-pyrrole dimer clusters have been studied by the dispersion-corrected density functional theory(DFT) calculations. Two distinct types of hydrogen bonds are demonstrated with optimized geometric structures and largest interaction energy moduli. Comprehensive spectroscopic analysis is also addressed revealing the orientation-dependent interactions by noting the altered red-shifts of the infrared and Raman activities. Then we employ natural bond orbital(NBO)analysis and atom in molecules(AIM) theory to have determined the origin and relative energetic contributions of the weak interactions in these systems. NBO and AIM calculations confirm the V-shaped dimer cluster is dominated by N.H···N and C.H···π hydrogen bonds, while the J-aggregated isomer is stabilized by N.H···π, n→π* and weak π···π* stacking interactions.The noncovalent interactions are also demonstrated via energy decomposition analysis associated with electrostatic and dispersion contributions.     

1,2,4-三氮杂苯-(H2O)n复合物氢键相互作用的密度泛函理论研究

用密度泛函理论方法在B3LYP/6-31++G**水平上对1,2,4-三氮杂苯-(H₂O)_n (n＝1, 2, 3)氢键复合物的基态进行了结构优化和能量计算, 结果表明复合物之间存在较强的氢键作用, 所有稳定复合物结构中形成一个N…H—O氢键并终止于弱O…H—C氢键的氢键水链的构型最稳定. 同时, 用含时密度泛函理论方法(TD-DFT)在TD-B3LYP/6-31++G**水平上计算了1,2,4-三氮杂苯单体及其氢键复合物的单重态第一¹(n, π^*)垂直激发能.     

Supramolecular networks supported by the anion…π linkage of Keggin‐type heteropolyoxotungstates

Anion…π interactions are newly recognized weak supramolecular forces which are relevant to many types of electron‐deficient aromatic substrates. Being less competitive with respect to conventional hydrogen bonding, anion…π interactions are only rarely considered as a crystal‐structure‐defining factor. Their significance dramatically increases for polyoxometalate (POM) species, which offer extended oxide surfaces for maintaining dense aromatic/inorganic stacks. The structures of tetrakis(caffeinium) μ₁₂‐silicato‐tetracosa‐μ₂‐oxido‐dodecaoxidododecatungsten trihydrate, (C₈H₁₁N₄O₂)₄[SiW₁₂O₄₀]·3H₂O, (1), and tris(theobrominium) μ₁₂‐phosphato‐tetracosa‐μ₂‐oxido‐dodecaoxidododecatungsten ethanol sesquisolvate, (C₇H₉N₄O₂)₃[PW₁₂O₄₀]·1.5C₂H₅OH, (2), support the utility of anion…π interactions as a special kind of supramolecular synthon controlling the structures of ionic lattices. Both caffeinium [(HCaf)⁺ in (1)] and theobrominium cations [(HTbr)⁺ in (2)] reveal double stacking patterns at both axial sides of the aromatic frameworks, leading to the generation of anion…π…anion bridges. The latter provide the rare face‐to‐face linkage of the anions. In (1), every square face of the metal–oxide cuboctahedra accepts the interaction and the above bridges yield flat square nets, i.e. {(HCaf⁺)₂[SiW₁₂O₄₀]^4?}_n. Two additional cations afford single stacks only and they terminate the connectivity. Salt (2) retains a two‐dimensional (2D) motif of square nets, with anion…π…anion bridges involving two of the three (HTbr)⁺ cations. The remaining cations complete a fivefold anion…π environment of [PW₁₂O₄₀]^3?, acting as terminal groups. This single anion…π interaction is influenced by the specific pairing of (HTbr)⁺ cations by double amide‐to‐amide hydrogen bonding. Nevertheless, invariable 2D patterns in (1) and (2) suggest the dominant role of anion…π interactions as the structure‐governing factor, which is applicable to the construction of noncovalent linkages involving Keggin‐type oxometalates.     

The synergistic co‐operation of N—H…O=P hydrogen bonds and C—H…OX weak intermolecular interactions (X is =P or —C) in the (CH3O)2P(O)(NH–NHC6F5) amidophosphoester: a combined X‐ray crystallographic and theoretical study

The asymmetric unit of O,O′‐dimethyl [(2,3,4,5,6‐pentafluorophenyl)hydrazinyl]phosphonate, C₈H₈F₅N₂O₃P, is composed of two symmetry‐independent molecules with significant differences in the orientations of the C₆F₅ and OMe groups. In the crystal structure, a one‐dimensional assembly is mediated from classical N—H…O hydrogen bonds, which includes R₂²(8), D(2) and some higher‐order graph‐set motifs. By also considering weak C—H…O=P and C—H…O—C intermolecular interactions, a two‐dimensional network extends along the ab plane. The strengths of the hydrogen bonds were evaluated using quantum chemical calculations with the GAUSSIAN09 software package at the B3LYP/6‐311G(d,p) level of theory. The LP(O) to σ*(NH) and σ*(CH) charge‐transfer interactions were examined according to second‐order perturbation theory in natural bond orbital (NBO) methodology. The hydrogen‐bonded clusters of molecules, including N—H…O and C—H…O interactions, were constructed as input files for the calculations and the strengths of the hydrogen bonds are as follows: N—H…O [R₂²(8)] > N—H…O [D(2)] > C—H…O. The decomposed fingerprint plots show that the contribution portions of the F…H/H…F contacts in both molecules are the largest.     

Synthesis,photophysical, electrochemical and single-crystal x-ray diffraction study of (Z)-2-phenyl-3-(5-(4-(thiophen-2-yl)benzo[c][1,2,5]thiadiazol-7-yl)thiophen-2-yl)acrylonitrile

The optical characteristics, redox properties, thermogravimetric stability and single-crystal X-ray diffraction study of (Z)-2-phenyl-3-(5-(4-(thiophen-2-yl)benzo[c][1,2,5]thiadiazol-7-yl)thiophen-2-yl)acrylonitrile are examined using ultraviolet–visible spectrophotometry, cyclic voltammetry, thermal gravimetric analysis–diffraction scanning calorimetry analysis, single-crystal X-ray diffraction and density functional theory calculations. Evidently, the crystal structure of compound 6 is sustained by a number of weak nonconventional intermolecular forces of attraction such as C-H … N, C-H … π donor–acceptor interactions.     

Evaluation of N—H…S and N—H…π interactions in O,O′‐diethyl N‐(2,4,6‐trimethylphenyl)thiophosphate: a combination of X‐ray crystallographic and theoretical studies

In the crystal structure of O,O′‐diethyl N‐(2,4,6‐trimethylphenyl)thiophosphate, C₁₃H₂₂NO₂PS, two symmetrically independent thiophosphoramide molecules are linked through N—H…S and N—H…π hydrogen bonds to form a noncentrosymmetric dimer, with Z′ = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06‐2X level within the 6‐311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N—H…S hydrogen bond is slightly stronger than the N—H…π hydrogen bond. This is reflected in differences between the calculated N—H stretching frequencies of the isolated molecules and the frequencies of the same N—H units involved in the different hydrogen bonds of the hydrogen‐bonded dimer. For these hydrogen bonds, the corresponding charge transfers, i.e. lp (or π)→σ*, were studied, according to the second‐order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.     

A luminescent bis(pyridyl)‐substituted benzimidazole platinum(II) complex exhibiting an intermolecular anagostic interaction

The photophysical properties of transition metal complexes of the 5,6‐dimethyl‐2‐(pyridin‐2‐yl)‐1‐(pyridin‐2‐ylmethyl)‐1H‐benzimidazole ligand are of interest. Dichlorido[5,6‐dimethyl‐2‐(pyridin‐2‐yl)‐1‐(pyridin‐2‐ylmethyl)‐1H‐benzimidazole‐κ²N ²,N ³]platinum(II), [PtCl₂(C₂₀H₁₈N₄)], is luminescent in the solid state at room temperature. The compound displays a distorted square‐planar coordination geometry. The Pt—N(imidazole) bond length is shorter than the Pt—N(pyridine) bond length. The extended structure reveals that symmetry‐related molecules display weak C—H…N, C—H…Cl, and C—H…Pt hydrogen‐bonding interactions that are clearly discernable in the Hirshfeld surface and fingerprint plots. The intermolecular C—H…Pt and C—H…N interactions have been explored using density functional theory. The result of an analysis of the distance dependence of C—H…Pt yields a value consistent with that observed in the solid‐state structure. The energy of interaction for the C—H…Pt interaction is found to be about −11 kJ mol⁻¹.     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Structural and computational analysis of intermolecular interactions in a new 2‐thiouracil polymorph

The crystallization and characterization of a new polymorph of 2‐thiouracil by single‐crystal X‐ray diffraction, Hirshfeld surface analysis and periodic density functional theory (DFT) calculations are described. The previously published polymorph (A ) crystallizes in the triclinic space group P , while that described herein (B ) crystallizes in the monoclinic space group P 2₁/c . Periodic DFT calculations showed that the energies of polymorphs A and B , compared to the gas‐phase geometry, were −108.8 and −29.4 kJ mol⁻¹, respectively. The two polymorphs have different intermolecular contacts that were analyzed and are discussed in detail. Significant differences in the molecular structure were found only in the bond lengths and angles involving heteroatoms that are involved in hydrogen bonds. Decomposition of the Hirshfeld fingerprint plots revealed that O…H and S…H contacts cover over 50% of the noncovalent contacts in both of the polymorphs; however, they are quite different in strength. Hydrogen bonds of the N—H…O and N—H…S types were found in polymorph A , whereas in polymorph B , only those of the N—H…O type are present, resulting in a different packing in the unit cell. QTAIM (quantum theory of atoms in molecules) computational analysis showed that the interaction energies for these weak‐to‐medium strength hydrogen bonds with a noncovalent or mixed interaction character were estimated to fall within the ranges 5.4–10.2 and 4.9–9.2 kJ mol⁻¹ for polymorphs A and B , respectively. Also, the NCI (noncovalent interaction) plots revealed weak stacking interactions. The interaction energies for these interactions were in the ranges 3.5–4.1 and 3.1–5.5 kJ mol⁻¹ for polymorphs A and B , respectively, as shown by QTAIM analysis.