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1.
Vratislav Langer Eva Scholtzov Dalma Gyepesov Jozef Lusto Juraj Kronek 《Acta Crystallographica. Section C, Structural Chemistry》2007,63(3):o187-o189
In the crystal structure of the title compound, C9H9NO3, there are strong intramolecular O—H⋯N and intermolecular O—H⋯O hydrogen bonds which, together with weak intermolecular C—H⋯O hydrogen bonds, lead to the formation of infinite chains of molecules. The calculated intermolecular hydrogen‐bond energies are −11.3 and −2.7 kJ mol−1, respectively, showing the dominant role of the O—H⋯O hydrogen bonding. A natural bond orbital analysis revealed the electron contribution of the lone pairs of the oxazoline N and O atoms, and of the two hydroxy O atoms, to the order of the relevant bonds. 相似文献
2.
Lesaw Siero Maria Bukowska‐Strzyewska 《Acta Crystallographica. Section C, Structural Chemistry》2000,56(1):19-21
In the title dimeric complex, [Cu2(C4H4O4)2(C7H6N2S)4], which possesses a centre of symmetry, the Cu atoms are enclosed in a 14‐membered ring. They adopt a distorted square‐bipyramidal (4+2) coordination. The four closest donor atoms are two N atoms of 2‐aminobenzothiazole ligands and two O atoms of the succinate carboxylate groups. They form a square‐planar cis arrangement, with an average Cu—N distance of 2.003 (3) Å and Cu—O distances of 1.949 (3) and 1.965 (3) Å. Two longer Cu—O bonds of 2.709 (3) and 2.613 (3) Å involving the remaining O atoms of the carboxylate groups complete the sixfold coordination of the Cu atoms. The H atoms of each amino group of the 2‐aminobenzothiazole molecules form intra‐ and intermolecular N—H?O hydrogen bonds. A nearly perpendicular intermolecular C—H?Cg interaction (Cg is the centroid of the imidazole ring) is observed. The intramolecular Cu?Cu distance is 6.384 (2) Å. 相似文献
3.
Lei Yu Yuhua Wang Zhengguo Huang Hongke Wang Yumei Dai 《International journal of quantum chemistry》2012,112(5):1514-1525
The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρb) and its Laplace (?2ρb) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρb has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012 相似文献
4.
《Acta Crystallographica. Section C, Structural Chemistry》2017,73(7):508-516
In the structure of 2‐(4‐chloroanilino)‐1,3,2λ4‐diazaphosphol‐2‐one, C12H11ClN3OP, each molecule is connected with four neighbouring molecules through (N—H)2…O hydrogen bonds. These hydrogen bonds form a tubular arrangement along the [001] direction built from R 33(12) and R 43(14) hydrogen‐bond ring motifs, combined with a C (4) chain motif. The hole constructed in the tubular architecture includes a 12‐atom arrangement (three P, three N, three O and three H atoms) belonging to three adjacent molecules hydrogen bonded to each other. One of the N—H groups of the diazaphosphole ring, not co‐operating in classical hydrogen bonding, takes part in an N—H…π interaction. This interaction occurs within the tubular array and does not change the dimension of the hydrogen‐bond pattern. The energies of the N—H…O and N—H…π hydrogen bonds were studied by NBO (natural bond orbital) analysis, using the experimental hydrogen‐bonded cluster of molecules as the input file for the chemical calculations. In the 1H NMR experiment, the nitrogen‐bound proton of the diazaphosphole ring has a high value of 17.2 Hz for the 2J H–P coupling constant. 相似文献
5.
《Acta Crystallographica. Section C, Structural Chemistry》2018,74(7):847-855
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. 相似文献
6.
Anthony Linden Yuehui Zhou Heinz Heimgartner 《Acta Crystallographica. Section C, Structural Chemistry》2014,70(5):482-487
In the selenium‐containing heterocyclic title compound {systematic name: N‐[5‐(morpholin‐4‐yl)‐3H‐1,2,4‐diselenazol‐3‐ylidene]benzamide}, C13H13N3O2Se2, the five‐membered 1,2,4‐diselenazole ring and the amide group form a planar unit, but the phenyl ring plane is twisted by 22.12 (19)° relative to this plane. The five consecutive N—C bond lengths are all of similar lengths [1.316 (6)–1.358 (6) Å], indicating substantial delocalization along these bonds. The Se...O distance of 2.302 (3) Å, combined with a longer than usual amide C=O bond of 2.252 (5) Å, suggest a significant interaction between the amide O atom and its adjacent Se atom. An analysis of related structures containing an Se—Se...X unit (X = Se, S, O) shows a strong correlation between the Se—Se bond length and the strength of the Se...X interaction. When X = O, the strength of the Se...O interaction also correlates with the carbonyl C=O bond length. Weak intermolecular Se...Se, Se...O, C—H...O, C—H...π and π–π interactions each serve to link the molecules into ribbons or chains, with the C—H...O motif being a double helix, while the combination of all interactions generates the overall three‐dimensional supramolecular framework. 相似文献
7.
NO2气相硝化金刚烷的计算研究 总被引:3,自引:0,他引:3
运用密度泛函理论(DFT)和半经验MO-PM3方法研究了NO2气相硝化金刚烷反应机理. 计算结果表明, NO2不能直接取代金刚烷H; 在B3LYP/6-311++G(3df,2pd)//B3LYP/6-31G* 较高水平下, 对三个可能机理的反应势垒(Ea)的精确计算表明, 该反应的决速步骤为NO2中O和N进攻1-H的竞争过程, 且1-硝基金刚烷为主要产物. NO2中O进攻1-H决速反应过程中, 分子几何、原子自然电荷及IR光谱变化表明, C—H键的断裂和N—H键的形成是一个协同过程; 参与新键形成和旧键断裂原子C(1), H(11), O(28), O(29)和N(27)的原子自然电荷及与其相关的键长、键角有明显的变化. 反应过程中体系偶极矩的变化表明, 极性溶剂能降低反应势垒, 有利于反应的进行. 相似文献
8.
在DFT-B3LYP/6-311++G**水平上分别求得(CH3)2S…ClOH卤键复合物和(CH3)2S…HOCl氢键复合物势能面上的稳定构型. 频率分析表明, 与单体HOCl相比, 在两种复合物中, 10Cl—11O和12H—11O键伸缩振动频率发生显著的红移. 经MP2/6-311++G**水平计算的含基组重叠误差(BSSE)校正的气相中相互作用能分别为-11.69和-24.16 kJ·mol-1. 自然键轨道理论(NBO)分析表明, 在(CH3)2S…ClOH卤键复合物中, 引起10Cl—11O键变长的因素包括两种电荷转移: (i) 孤对电子LP(1S)1→σ*(10Cl—11O); (ii) 孤对电子LP(1S)2→σ*(10Cl—11O), 其中孤对电子LP(1S)2→σ*(10Cl—11O)转移占主要作用, 总的结果是使σ*(10Cl—11O)的自然布居数增加0.14035e, 同时11O原子的再杂化使其与10Cl成键时s成分增加, 即具有与电荷转移作用同样的“拉长效应”; 在(CH3)2S…HOCl氢键复合物中也存在类似的电荷转移, 但是11O原子的再杂化不同于前者. 自然键共振理论(NRT)进行键序分析表明, 在卤键复合物和氢键复合物中, 10Cl—11O和12H—11O键的键序都减小. 通过分子中原子理论(AIM)分析了复合物中卤键和氢键的电子密度拓扑性质. 相似文献
9.
Ligia R. Gomes John Nicolson Low Fernanda Borges Fernando Cagide 《Acta Crystallographica. Section C, Structural Chemistry》2013,69(8):927-933
The title compound, C17H13NO4, crystallizes in two polymorphic forms, each with two molecules in the asymmetric unit and in the monoclinic space group P21/c. All of the molecules have intramolecular hydrogen bonds involving the amide group. The amide N atoms act as donors to the carbonyl group of the pyrone and also to the methoxy group of the benzene ring. The carbonyl O atom of the amide group acts as an acceptor of the β and β′ C atoms belonging to the aromatic rings. These intramolecular hydrogen bonds have a profound effect on the molecular conformation. In one polymorph, the molecules in the asymmetric unit are linked to form dimers by weak C—H...O interactions. In the other, the molecules in the asymmetric unit are linked by a single weak C—H...O hydrogen bond. Two of these units are linked to form centrosymmetric tetramers by a second weak C—H...O interaction. Further interactions of this type link the molecules into chains, so forming a three‐dimensional network. These interactions in both polymorphs are supplemented by π–π interactions between the chromone rings and between the chromone and methoxyphenyl rings. 相似文献
10.
Akbar Raissi Shabari Mehrdad Pourayoubi Pari Marandi Michal Duek Vclav Eigner 《Acta Crystallographica. Section C, Structural Chemistry》2015,71(4):338-343
The structure of N,N′,N′′‐tribenzylphosphorothioic triamide, C21H24N3PS, (I), and analysis of the bond‐angle sums at the N atoms for this compound, and for 74 structures with a P(S)[N]3 skeleton and the N atom in a three‐coordinate geometry found in the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53 , 662–671], are reported. For (I), the bond‐angle sum at one of the N atoms [359 (1)°] shows a nearly planar configuration, while the other two show a nonplanar geometry with bond‐angle sums of 342 (1) and 347 (1)°. The location of the atoms attached to the nonplanar N atoms suggests an anti orientation of the corresponding lone electron pairs (LEPs) on these N atoms with respect to the P=S group. For 74 structures with a P(S)[N]3 skeleton and with the N atom in a three‐coordinate geometry, the bond‐angle sums at the N atoms were found to be in the range 293–360°. Among 307 such three‐coordinate N atoms, 39% (120 N atoms) have bond‐angle sums in the range 359–360°, in accordance with sp2 hybridization, and 45% (138 N atoms) have bond‐angle sums in the range 352–359°, with hybridization close to sp2. For the orientation of the LEP with respect to the P=S group, the anti orientation was found to be a general rule for N atoms, with the corresponding bond‐angle sums deviating by more than 8° from the planar value of 360°. In the title structure, the S atom takes part in intermolecular (N—H...)(N—H...)S hydrogen bonds, connecting the molecules into extended chains parallel to the b axis. The co‐operation of one N atom in an N—H...S hydrogen bond as an H‐atom donor, and in an N—H...N hydrogen bond as an acceptor, is a novel feature of the crystal structure. 相似文献
11.
V. H. Rodrigues J. A. Paixo M. M. R. R. Costa A. Matos Beja 《Acta Crystallographica. Section C, Structural Chemistry》2001,57(4):417-420
In the title compound, C4H10NO2+·C2F3O2?, the main N—C—COOH skeleton of the protonated amino acid is nearly planar. The C=O/C—N and C=O/O—H bonds are syn and the two methyl groups are gauche to the methylene H atoms. The conformation of the cation in the crystal is compared to that given by ab initio calculations (Hartree–Fock, self‐consistent field molecular‐orbital theory). The trifluoroacetate anion has the typical staggered conformation with usual bond distances and angles. The cation and anion form dimers through a strong O—H?O hydrogen bond which are further interconnected in infinite zigzag chains running parallel to the a axis by N—H?O bonds. Weaker C—H?O interactions involving the methyl groups and the carboxy O atoms of the cation occur between the chains. 相似文献
12.
Shun‐ichi Kawahara Chojiro Kojima Kazunari Taira Tadafumi Uchimaru 《Helvetica chimica acta》2003,86(10):3265-3273
trans‐Hydrogen‐bond hyperfine splitting via magnetic interaction, which is observed as J‐coupling in NMR experiments, was theoretically studied. trans‐Hydrogen‐bond hyperfine splitting should be closely related to the orbital interaction between the lone‐pair orbital of the H‐bond acceptor and the antibond orbital of the H‐bond donor. A linear relationship was observed between magnetic interaction hyperfine splitting through a H‐bond and the H‐bond strength. The relationship was dependent on the type of the nucleus forming the H‐bond; linear correlation was observed in N H⋅⋅⋅O/N type or O H⋅⋅⋅N type H‐bonded complexes, but not in O H⋅⋅⋅O type H‐bonded complexes. 相似文献
13.
Wenhui Zhang Reagan J. Meredith Allen G. Oliver Ian Carmichael Anthony S. Serianni 《Acta Crystallographica. Section C, Structural Chemistry》2020,76(3):287-297
The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C15H27NO11·H2O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter. 相似文献
14.
《Chemistry (Weinheim an der Bergstrasse, Germany)》2003,9(13):3112-3121
The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has Cs symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρb and Hb of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom. 相似文献
15.
Pavel Mach Vratislav Langer Eva Scholtzov Tom Sol
an
ubomír Smr
ok 《Acta Crystallographica. Section C, Structural Chemistry》2006,62(9):o544-o546
Molecules of the title compound, C11H10N2O, are effectively planar. In the crystal structure, they are stabilized primarily by electrostatic interactions, as the dipole moment of the molecule is 4.56 D. In addition, the molecules are linked by weak C—H⋯N and C—H⋯O hydrogen bonds. An analysis of bonding conditions in the molecule was carried out using natural bond orbital (NBO) formalism. 相似文献
16.
A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes 下载免费PDF全文
Shu‐Shi Li Cui‐Ying Huang Jiao‐Jiao Hao Chang‐Sheng Wang 《Journal of computational chemistry》2014,35(6):415-426
In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc. 相似文献
17.
Lourdes Urpí Katia Jimnez Xavier Solans Alfonso Rodríguez‐Galn Jordi Puiggalí 《Acta Crystallographica. Section C, Structural Chemistry》2003,59(1):o24-o26
The β‐alanine residue of the title compound, C5H8ClNO3, has a ggt folded conformation, which is mainly stabilized through intermolecular N—H⋯O=C (amide–acid) and O—H⋯O=C (acid–amide) hydrogen bonds. In addition, a cis conformation is found for the Cl—CH2—C(=O)—NH torsion angle, which is associated with the presence of an intramolecular hydrogen bond. 相似文献
18.
Jun Sakamoto Takashi Nakagawa Nobuko Kanehisa Yasushi Kai Masahiro Katsura 《Acta Crystallographica. Section C, Structural Chemistry》2000,56(9):e413-e413
The crystal structure of 3‐chloropropionamide, C3H6ClNO, (I), was determined in order to obtain coordinates for molecular‐orbital calculations. Intermolecular N—H?O and C—H?O hydrogen bonds link the molecules into continuous two‐dimensional sheets parallel to the (100) plane. The bond distances are C—Cl 1.793 (3), C=O 1.233 (3) and C—N 1.320 (3) Å. 相似文献
19.
Andrei V. Afonin Igor A. Ushakov Alexander V. Vashchenko Evgeniy V. Kondrashov Alexander Yu. Rulev 《Magnetic resonance in chemistry : MRC》2010,48(9):661-670
In the series of diaminoenones, large high‐frequency shifts of the 1H NMR of the N? H group in the cis‐position relative to the carbonyl group suggests strong N? H···O intramolecular hydrogen bonding comprising a six‐membered chelate ring. The N? H···O hydrogen bond causes an increase of the 1J(N,H) coupling constant by 2–4 Hz and high‐frequency shift of the 15N signal by 9–10 ppm despite of the lengthening of the relevant N? H bond. These experimental trends are substantiated by gauge‐independent atomic orbital and density functional theory calculations of the shielding and coupling constants in the 3,3‐bis(isopropylamino)‐1‐(aryl)prop‐2‐en‐1‐one (12) for conformations with the Z‐ and E‐orientations of the carbonyl group relative to the N? H group. The effects of the N? H···O hydrogen‐bond on the NMR parameters are analyzed with the atoms‐in‐molecules (AIM) and natural bond orbital (NBO) methods. The AIM method indicates a weakening of the N? H···O hydrogen bond as compared with that of 1,1‐di(pyrrol‐2‐yl)‐2‐formylethene (13) where N? H···O hydrogen bridge establishes a seven‐membered chelate ring, and the corresponding 1J(N,H) coupling constant decreases. The NBO method reveals that the LP(O) →σ*N? H hyperconjugative interaction is weakened on going from the six‐membered chelate ring to the seven‐membered one due to a more bent hydrogen bond in the former case. A dominating effect of the N? H bond rehybridization, owing to an electrostatic term in the hydrogen bonding, seems to provide an increase of the 1J(N,H) value as a consequence of the N? H···O hydrogen bonding in the studied diaminoenones. Copyright © 2010 John Wiley & Sons, Ltd. 相似文献
20.
在DFT-B3LYP及MP2/6-311++G**水平上分别求得CH3SH…HOCl氢键复合物和CH3SH…ClOH卤键复合物势能面上的稳定构型. 频率分析表明, 与单体HOCl相比, 在两种复合物中, Cl(9)—O(7)和H(8)—O(7)键伸缩振动频率发生显著的红移. 经MP2/6-311++G**水平计算的含基组重叠误差(BSSE)校正的气相中相互作用能分别为-19.23和-6.85 kJ8226;mol-1. 自然键轨道理论(NBO)分析表明, 在CH3SH…ClOH卤键复合物中, 引起Cl(9)—O(7)键变长的因素包括2种电荷转移: (i)孤对电子LP[S(1)]1→σ*[Cl(9)—O(7)]; (ii)孤对电子LP[S(1)]2→σ*[Cl(9)—O(7)], 其中孤对电子LP[S(1)]2→σ*[Cl(9)—O(7)]转移占主要作用, 总的结果是使σ*[Cl(10)—O(11)]的自然布居数增加, 同时O(7)和Cl(9)原子s成分均增加的杂化重优具有与电荷转移作用相同的“拉长效应”; 在CH3SH…HOCl氢键复合物中也存在类似的电荷转移, 但是O(7)原子的再杂化效应不同于前者. 自然键共振理论(NRT)进行键序分析表明, 在氢键复合物和卤键复合物中, H(8)—O(7)和Cl(9)—O(7)键的键序都减小. 通过分子中原子理论(AIM)分析了复合物中氢键和卤键的电子密度拓扑性质. 相似文献