X-ray scattering and density-functional theory calculations to study the presence of hydrogen-bonded clusters in liquid N-methylacetamide

A structural investigation of liquid N-methylacetamide (NMA) is performed by x-ray scattering and density functional theory (DFT). Experimental data are analyzed to yield the total structure function SM(Q) and the pair correlation function g(r). The DFT calculations, using the standard triple zeta valence basis set augmented by a diffuse function for carbon, nitrogen and oxygen atoms, are performed on the one hand to study the structure and stability of the two possible conformers cis and trans. On the other hand, they are meant to examine some possible clusters which may describe the intermolecular arrangement in liquid NMA. Among two series of dimers and trimers associations, the spectra are particularly interpreted in terms of: Trans NMA dimers and trimers which resemble the short-range crystal structure, mixed cis and trans trimers and cis cyclic trimers. The H-bonding parameters and the intermolecular energy for each model are described.     

Intermolecular association in liquid N-methylacetamide as studied by x-ray scattering

A structural investigation of liquid N methylacetamide was performed at 308 K using x-ray scattering. To extract the molecular form factor F1(q), the geometry of the conformer which has been found in the crystal is considered. The intermolecular structure function DM(q) is interpreted in terms of H-bonding interactions. The crystal N...O distance is taken into accounted and the number of H bond(s) is assumed to be, respectively, equal to one and two. The liquid structure can be described by a linear dimer or chainlike trimer similar to the ones existing in the crystal. The structure factors SM(q) extracted from these clusters fairly agree with the experimental one beyond q=2.5 A(-1).     

Mimicking trimeric interactions in the aromatic side chains of the proteins: a gas phase study of indole...(pyrrole)2 heterotrimer

Aromatic trimeric interactions are extremely significant in the stabilization of the specific structures of the proteins as well as protein-protein, and protein-ligand interactions. Here we have reported a direct evidence of the observation of a cyclic asymmetric structure of indole...(pyrrole)(2) trimer bound by three N-H...π hydrogen bonding interactions in a supersonic jet. The experiment has been performed by using resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques. Density functional theory (DFT) calculations nicely corroborate the experimental results showing one weakly allowed IR-active band due to symmetric stretch of the N-H bonds and two strongly allowed IR-active bands due to two types of asymmetric stretches of the N-H bonds in the trimer. The present spectroscopic investigation demonstrates that the strength of the three N-H...π bound intermolecular interactions in the cyclic asymmetric trimer is quite different unlike the corresponding interactions of similar strength in a cyclic symmetric trimer.     

Liquid structure of room-temperature ionic liquid, 1-Ethyl-3-methylimidazolium bis-(trifluoromethanesulfonyl) imide

The liquid structure of 1-ethyl-3-methylimidazolium bis-(trifluoromethanesulfonyl) imide (EMI(+)TFSI(-)) has been studied by means of large-angle X-ray scattering (LAXS), (1)H, (13)C, and (19)F NMR, and molecular dynamics (MD) simulations. LAXS measurements show that the ionic liquid is highly structured with intermolecular interactions at around 6, 9, and 15 A. The intermolecular interactions at around 6, 9, and 15 A are ascribed, on the basis of the MD simulation, to the nearest neighbor EMI(+)...TFSI(-) interaction, the EMI(+)...EMI(+) and TFSI(-)...TFSI(-) interactions, and the second neighbor EMI+...TFSI(-) interaction, respectively. The ionic liquid involves two conformers, C(1) (cis) and C(2) (trans), for TFSI(-), and two conformers, planar cis and nonplanar staggered, for EMI(+), and thus the system involves four types of the EMI(+)...TFSI(-) interactions in the liquid state by taking into account the conformers. However, the EMI(+)...TFSI(-) interaction is not largely different for all combinations of the conformers. The same applies alsoto the EMI(+)...EMI(+) and TFSI(-)...TFSI(-) interactions. It is suggested from the 13C NMR that the imidazolium C(2) proton of EMI(+) strongly interacts with the O atom of the -SO(2)(CF(3)) group of TFSI(-). The interaction is not ascribed to hydrogen-bonding, according to the MD simulation. It is shown that the liquid structure is significantly different from the layered crystal structure that involves only the nonplanar staggered EMI(+) and C(1) TFSI(-) conformers.     

Ab initio and DFT studies on van der Waals trimers: the OCS.(CO2)2 complexes

Ab initio calculations [MP2, MP4SDTQ, and QCISD(T)] using different basis sets [6-31G(d,p), cc-pVXZ (X = D, T, Q), and aug-cc-pVDZ] and density functional theory [B3LYP/6-31G(d,p)] calculations were carried out to study the OCS.(CO2)2 van der Waals trimer. The DFT has proved inappropriate to the study of this type of systems where the dispersion forces are expected to play a relevant role. Three minima isomers (two noncyclic and one cyclic) were located and characterized. The most stable isomer exhibits a noncyclic barrel-like structure whose bond lengths, angles, rotational constants, and dipole moment agree quite well with the corresponding experimental values of the only structure observed in recent microwave spectroscopic studies. The energetic proximity of the three isomers, with stabilization energies of 1442, 1371, and 1307 cm-1, respectively, at the CBS-MP2/cc-pVXZ (X = D, T, Q) level, strongly suggests that the two unobserved structures should also be detected as in the case of the (CO2)3 trimer where both noncyclic and cyclic isomers have been reported to exist. The many-body symmetry-adapted perturbation theory is employed to analyze the nature of the interactions leading to the formation of the different structures. The three-body contributions are small and stabilizing for the two most stable structures and almost negligible for the cyclic isomer.     

1-萘酚的紫外共振双光子电离光谱

利用脉冲分子束技术, 在305-322 nm范围内研究了1-萘酚(1NP)的共振双光子电离(R2PI)光谱. 1NP分子存在cis和trans两种旋转异构体, 但实验中仅观测到trans异构体的电子振动跃迁光谱, 其S1←S0跃迁的(0-0)带头出现在317.90 nm(即31456 cm-1)位置. 利用光谱选律及ab initio和密度泛函(DFT)计算, 对trans异构体在S1态的振动模进行标识, 得出主要对应于对称性为a'的平面内振动模. 计算显示, cis异构体在电子基态S0的能量较trans异构体高出439 cm-1, 而第一激发能却比trans异构体的低1216 cm-1, 与之相应的实验值分别是220和274 cm-1. 计算数值与实验结果在能量变化趋势上完全一致. 共振双光子电离谱中没有观测到cis异构体的光谱信号, 其原因可归结为分子束的有效冷却效应使得处于基态的cis异构体的布居数密度相对trans异构体极低, 导致cis光谱信号太小而未能被探测到.     

Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs

Due to the presence of the 2'-OH hydroxyl group of ribose, RNA molecules utilize an astonishing variability of base pairing patterns to build up their structures and perform the biological functions. Many of the key RNA base pairing families have no counterparts in DNA. In this study, the trans Watson-Crick/sugar edge (trans WC/SE) RNA base pair family has been characterized using quantum chemical and molecular mechanics calculations. Gas-phase optimized geometries from density functional theory (DFT) calculations and RIMP2 interaction energies are reported for the 10 crystallographically identified trans WC/SE base pairing patterns. Further, stable structures are predicted for all of the remaining six possible members of this family not seen in RNAs so far. Among these novel six base pairs, the computations substantially refine two structures suggested earlier based on simple isosteric considerations. For two additional trans WC/SE base pairs predicted in this study, no arrangement was suggested before. Thus, our study brings a complete set of trans WC/SE base pairing patterns. The present results are also contrasted with calculations reported recently for the cis WC/SE base pair family. The computed base pair sizes are in sound correlation with the X-ray data for all WC/SE pairing patterns including both their cis and trans isomers. This confirms that the isostericity of RNA base pairs, which is one of the key factors determining the RNA sequence conservation patterns, originates in the properties of the isolated base pairs. In contrast to the cis structures, however, the isosteric subgroups of the trans WC/SE family differ not only in their H-bonding patterns and steric dimensions but also in the intrinsic strength of the intermolecular interactions. The distribution of the total interaction energy over the sugar-base and base-base contributions is controlled by the cis-trans isomerism.     

ClC(O)NCS分子振动光谱的理论研究

采用密度泛函理论DFT(B3LYP)方法,以6-31G^*为基组对ClC(O)NCS的反式和顺式两种构型的几何结构、振动谐性力场和红外光谱进行了研究.B3LYP/6-31G^*的理论力场由适用于B3LYP/6-31G^*计算水平和大多数有机分子的一套固定标度因子进行标度.根据标度后的理论力场进行简正坐标分析得到的势能分布(PED)和红外光谱强度值对ClC(O)NCS分子的顺式和反式两种构型的振动基频进行了理论归属.     

NMR and theoretical calculations: a unified view of the cis/trans isomerization of 2-substituted thiazolidines containing peptides

The cis/trans isomerization of peptides containing the pseudoproline (4R)-thiazolidine-4-carboxylic acid Cys(Psi (R1,R2) pro) is investigated from both an experimental and a theoretical point of view by NMR and DFT calculations. A series of Ac-Cys(Psi(R1,R2) pro)-OCH3 and Ac-Cys(Psi(R1,R2) pro)-NHCH3 peptides were prepared to assess the influence of the substitution at the C2 position as well as of the amide following the thiazolidine residue. For each compound, the cis/trans ratio along with free energy, the puckering of the thiazolidine ring and the free rotational energy barrier are reported and discussed. We observe there is a pronounced effect of the C2 substituents and of the chirality upon the cis/trans ratio with the population of the cis content in the order (2R)-Cys(Psi(CH3,H) pro)<(2S)-Cys(Psi(H,CH3) pro)相似文献   

新的钌环丙烷化催化体系的探索(Ⅱ) 氮膦配体立体化学结构控制顺反比选择性的初步研究

本文研究了一个新的钌催化的苯乙烯环丙烷化反应催化体系。当该催化体系用三氟甲磺酸银预处理后其催化的环丙烷化反应产物的顺反比接近1：1,且顺式产物略微占优。这在环丙烷化反应中是不多见的。我们用分子力学／动力学对该催化体系进行了模拟。结果表明键能并非是决定产物顺反比的主要因素,但是对于非键能来说,由于中间体M1与苯乙烯作用生成顺式产物时的范德华作用非常强,它弥补了由静电能所引起的能量上的不利因素。所以总能量对生成顺式产物较为有利。但是由于生成顺式产物与反式产物的总能量差别不大（2．5kcal.mol^-1),所以环丙烷化产物的顺反比接近1：1。这是氮膦配体立体化学结构控制产物选择性的结果。     

Trifluoromethoxycarbonyl peroxynitrate, CF3OCOOONO2

The trioxide, CF(3)OC(O)OOOC(O)OCF(3), reacts with NO(2) at 0 degrees C to yield the new peroxynitrate, CF(3)OC(O)OONO(2), which is stable for hours at room temperature. It is spectroscopically characterized and some thermal properties are reported. From the vapor pressure, ln(p/p(0)) = 14.06 - 4565/T, of the liquid above the melting point of -89 degrees C, the extrapolated boiling point is 52 degrees C. CF(3)OC(O)OONO(2) dissociates at higher temperatures and low pressures into the radicals CF(3)OC(O)OO and NO(2) as demonstrated by matrix isolation experiments. The matrix-isolated peroxy radicals consist in a rotameric mixture of trans,trans,trans-CF(3)OC(O)OO and trans,trans,cis-CF(3)OC(O)OO, where trans and cis denote dihedral angles of ca. 180 degrees and 0 degree, respectively, around beta F-C-O-C, beta C-O-C-O, and beta O-C-O-O, with an equilibrium composition dependent on the thermolysis temperature. The radical trans,trans,cis-CF(3)OC(O)OO is found to be ca. 3 kJ mol(-1) higher in enthalpy than trans,trans,trans-CF(3)OC(O)OO. DFT calculations are performed to support the vibrational assignments and to provide structural information about CF(3)OC(O)OONO(2).     

Photoisomerization and photochemistry of matrix-isolated 3-furaldehyde

3-Furaldehyde (3FA) was isolated in an argon matrix at 12 K and studied using FTIR spectroscopy and quantum chemistry. The molecule has two conformers, with trans and cis orientation of the O=C-C=C dihedral angle. At the B3LYP/6-311++G(d,p) level of theory, the trans form was computed to be ca. 4 kJ mol(-1) more stable than the cis form. The relative stability of the two conformers was explained using the natural bond orbital (NBO) method. In fair agreement with their calculated relative energies and the high barrier of rotamerization (ca. 34 kJ mol(-1) from trans to cis), the trans and cis conformers were trapped in an argon matrix from the compound room temperature gas phase in proportion ~7:1. The experimentally observed vibrational signatures of the two forms are in a good agreement with the theoretically calculated spectra. Broad-band UV-irradiation (λ > 234 nm) of the matrix-isolated compound resulted in partial trans → cis isomerization, which ended at a photostationary state with the trans/cis ratio being ca. 1.85:1. This result was interpreted based on results of time-dependent DFT calculations. Irradiation at higher energies (λ > 200 nm) led to decarbonylation of the compound, yielding furan, cyclopropene-3-carbaldehyde, and two C(3)H(4) isomers: cyclopropene and propadiene.     

N-(1-萘基)琥珀酰亚胺分子间相互作用的计算机模拟

对分子间相互作用比较复杂的N-(1-萘基)琥珀酰亚胺进行理论计算时, 提出了将溶液构建和随机构象搜索相结合的多分子相互作用体系构建方法, 可以简单而准确地得到二聚体和三聚体结构, 其中二聚体结构和采用分子对接方法得到的结果完全一致. 经密度泛函理论计算, 得到了在真空条件下二聚体结构的最低能量构象. 对较大体系的三聚体结构采用高精度分子力学进行了理论计算. 通过分子间相互作用对分子构象的影响讨论了溶液结晶过程中N-(1-萘基)琥珀酰亚胺分子构象变化, 为该化合物结晶机理的深入研究提供重要依据.     

Antioxidant activity of hydroxystilbene derivatives in homogeneous solution

The antioxidant activity of the cis and trans isomers of several analogues of resveratrol and pterostilbene has been investigated, especially with regard to the effect of the stereochemistry about the olefinic double bond. The antioxidant power of these compounds was estimated by measuring the rate constants for their reactions with peroxyl radicals and, with two of them, the bond dissociation enthalpy (BDE) of the phenolic O-H bond which is cleaved in the inhibition reaction. The present data show that in homogeneous solution the various hydroxystilbenes investigated behave as mild antioxidants with the notable exceptions of the trans isomer of 4 and 6, whose activities are only slightly lower than that of alpha-tocopherol (vitamin E). The rate constants of the inhibition reaction show that the antioxidant activity of the cis-hydroxystilbene is in all the examined cases worse, by a factor ranging between 2 and 6, than that of the corresponding trans isomers. This lower reactivity depends on enthalpy factors as it can be inferred by the experimental values of the O-H bond dissociation enthalpy in the two geometric isomers of 3',5'-di-tert-butyl-4'-hydroxy-3,5-dimethoxystilbene showing that the strength of the O-H bond in the cis isomer is larger by 1.8 kcal/mol. DFT calculations provide a rationalization of this result, indicating that, although the cis geometry implies a destabilization with respect to the trans species of both phenoxyl radical and parent hydroxystilbene, the destabilization of the radical is larger because the folding of the structure strongly reduces the delocalization of the unpaired electron on the styryl group. A comparison of these results with previously reported data on the proapoptotic activity of these stilbenoids suggests that these two properties are not correlated.     

Photophysical studies of the trans to cis isomerization of the push-pull molecule: 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene (mepepy)

Organic molecules possessing intramolecular charge-transfer properties (D-pi-A type molecules) are of key interest particularly in the development of new optoelectronic materials as well as photoinduced magnetism. One such class of D-pi-A molecules that is of particular interest contains photoswitchable intramolecular charge-transfer states via a photoisomerizable pi-system linking the donor and acceptor groups. Here we report the photophysical and electronic properties of the trans to cis isomerization of 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene ligand (mepepy) in aqueous solution using photoacoustic calorimetry (PAC) and theoretical methods. Density functional theory (DFT) calculations demonstrate a global energy difference between cis and trans isomers of mepepy to be 8 kcal mol(-1), while a slightly lower energy is observed between the local minima for the trans and cis isomers (7 kcal mol(-1)). Interestingly, the trans isomer appears to exhibit two ground-state minima separated by an energy barrier of approximately 9 kcal mol(-1). Results from the PAC studies indicate that the trans to cis isomerization results in a negligible volume change (0.9 +/- 0.4 mL mol(-1)) and an enthalpy change of 18 +/- 3 kcal mol(-1). The fact that the acoustic waves associated with the trans to cis transition of mepepy overlap in frequency with those of a calorimetric reference implies that the conformational transition occurs faster than the approximately 50 ns response time of the acoustic detector. Comparison of the experimental results with theoretical studies provide evidence for a mechanism in which the trans to cis isomerization of mepepy results in the loss of a hydrogen bond between a water molecule and the pyridine ring of mepepy.     

Valence and spin situations in isomeric [(bpy)Ru(Q')2]n (Q' = 3,5-di-tert-butyl-N-aryl-1,2-benzoquinonemonoimine). An experimental and DFT analysis

The article deals with the ruthenium complexes, [(bpy)Ru(Q')(2)] (1-3) incorporating two unsymmetrical redox-noninnocent iminoquinone moieties [bpy = 2,2'-bipyridine; Q' = 3,5-di-tert-butyl-N-aryl-1,2-benzoquinonemonoimine, aryl = C(6)H(5) (Q'(1)), 1; m-Cl(2)C(6)H(3) (Q'(2)), 2; m-(OCH(3))(2)C(6)H(3) (Q'(3)), 3]. 1 and 3 have been preferentially stabilised in the cc-isomeric form while both the ct- and cc-isomeric forms of 2 are isolated [ct: cis and trans and cc: cis and cis with respect to the mutual orientations of O and N donors of two Q']. The isomeric identities of 1-3 have been authenticated by their single-crystal X-ray structures. The collective consideration of crystallographic and DFT data along with other analytical events reveals that 1-3 exhibit the valence configuration of [(bpy)Ru(II)(Q'(Sq))(2)]. The magnetization studies reveal a ferromagnetic response at 300 K and virtual diamagnetic behaviour at 2 K. DFT calculations on representative 2a and 2b predict that the excited triplet (S = 1) state is lying close to the singlet (S = 0) ground state with singlet-triplet separation of 0.038 eV and 0.075 eV, respectively. In corroboration with the paramagnetic features the complexes exhibit free radical EPR signals with g～2 and (1)HNMR spectra with broad aromatic proton signals associated with the Q' at 300 K. Experimental results in conjunction with the DFT (for representative 2a and 2b) reveal iminoquinone based preferential electron-transfer processes leaving the ruthenium(ii) ion mostly as a redox insensitive entity: [(bpy)Ru(II)(Q'(Q))(2)](2+) (1(2+)-3(2+)) ? [(bpy)Ru(II)(Q(')(Sq))(Q(')(Q))](+) (1(+)-3(+)) ? [(bpy)Ru(II)(Q(')(Sq))(2)] (1-3) ? [(bpy)Ru(II)(Q(')(Sq))(Q(')(Cat))](-)/[(bpy)Ru(III)(Q(')(Cat))(2)](-) (1(-)-3(-)). The diamagnetic doubly oxidised state, [(bpy)Ru(II)(Q'(Q))(2)](2+) in 1(2+)-3(2+) has been authenticated further by the crystal structure determination of the representative [(bpy)Ru(II)(Q'(3))(2)](ClO(4))(2) [3](ClO(4))(2) as well as by its sharp (1)H NMR spectrum. The key electronic transitions in each redox state of 1(n)-3(n) have been assigned by TD-DFT calculations on representative 2a and 2b.     

含冠醚环的席夫碱型液晶高分子的合成与表征

以 4 ,4′ (α ,ω 烷亚甲基二酰氧 )二苯甲醛和二氨基二苯并 14 冠 4为单体 ,采用溶液缩聚方法 ,首次合成了一类新的含冠醚环的席夫碱型液晶高分子 .一种单体采用脂族二酰氯和对羟基苯甲醛反应制备 ,另一种新的单体采用二硝基二苯并 14 冠 4 ,在钯 碳催化剂存在下 ,水合肼还原制备 .通过1H NMR、13 C NMR和分子力学计算方法研究了二氨基二苯并 14 冠 4的两种异构体的空间立体结构 ,发现能从1H NMR谱图上区分它们的立体结构 .它们的立体结构近似属于Cs 和C2 群 .聚合物的分子量不高 ,Mn 在 130 0 0～ 2 4 0 0 0之间 .单体的结构通过元素分析、IR、1H NMR和MS等方法确证 .聚合物的性质采用GPC、DSC、TG和POM等方法进行了研究 .发现所有的聚合物加热到各自的熔融温度 (Tm)以上都能形成液晶态 ,在液晶态可以观察到向列相的丝状织构和纹影织构 .聚合物的玻璃化转变温度 (Tg)、熔融温度和各向同性温度 (Ti)随聚合物分子中柔性间隔基的变化而变化 ,它们有较高的清亮点温度和宽的液晶态温度范围 .WAXD的研究进一步证实了聚合物的液晶性     

Is 2-cyclopropylpropene really gauche?

Infrared spectra of gaseous and solid 2-cyclopropylpropene (2-CPP, c-C3H5C (CH3)CH2) have been recorded from 3500 to 40 cm-1, and Raman spectra (3200-150 cm-1) of the liquid as well as mid-infrared spectra of 2-CPP in liquid krypton solution (from -105 to -150 degrees C) were also obtained. Ab initio calculations, with basis sets up to 6-311+G(2df, 2pd), were carried out for this molecule, using the restricted Hartree-Fock (RHF) approach, with full electron correlation by the perturbation method to second order (MP2(full)) and density functional theory (DFT) by the B3LYP method. The combination of the experimental and computational results (particularly with the higher basis sets) unequivocally identifies the more stable conformer of 2-CPP as the trans form, with the gauche rotamer higher in energy, but also stable. The cis structure of this compound is not observed experimentally, and is predicted by the computational approaches to be a transition state. By studying the temperature variation of two well-resolved sets of conformational doublets of 2-CPP dissolved in liquid krypton, an average enthalpy difference between conformers of 182+/-18 cm-1 (2.18+/-0.22 kJ mol-1) has been determined, with the trans conformation lower in energy in the fluid states, and the sole conformer present in the polycrystalline solid phase. This enthalpy difference corresponds to an ambient temperature conformational equilibrium in the fluid phases of 2-cyclopropylpropene containing approximately 55+/-2% of the more stable trans rotameric form. A complete vibrational assignment for the trans conformer of 2-CPP is given, and many of the bands of the gauche rotamer have also been assigned. Structural parameters, dipole moments, and rotational constants for this molecule have been calculated at the MP2(full)/6-311+G(d,p) level, and these results--as well as the results from the experimental studies--are compared to similar quantities in related compounds.     

Ã-X absorption of propargyl peroxy radical (H-C≡C-CH2OO·): a cavity ring-down spectroscopic and computational study

The ?-X electronic absorption spectrum of propargyl peroxy radical has been recorded at room temperature by cavity ring-down spectroscopy. Electronic structure calculations predict two isomeric forms, acetylenic and allenic, with two stable conformers for each. The acetylenic trans conformer, with a band origin at 7631.8 ± 0.1 cm(-1), is definitively assigned on the basis of ab initio calculations and rotational simulations, and possible assignments for the acetylenic gauche and allenic trans forms are given. A fourth form, allenic cis, is not observed. Simulations based on calculated torsional potentials predict that the allenic trans form will have a long, poorly resolved progression in the OOCC torsional vibration, consistent with experimental observations.