Local order in fully deuterated liquid N-methylacetamide (C3D7NO) as studied by neutron diffraction and density-functional theory calculations

A structural investigation of fully deuterated liquid N-methylacetmide (NMAd7) is performed at 308 K and atmospheric pressure by using neutron diffraction together with density-functional theory (DFT). The analysis of experimental data yields the total structure factor SM(Q), the molecular form factor F1(Q), and the distinct pair correlation function gL(r). The DFT calculations are performed to study the relative stability of the two possible isomers (trans and cis) and to examine some possible clusters recently published that may describe the intermolecular arrangement in the liquid state. Neutron measurements can be interpreted in terms of trans linear trimer (T1) and cis cyclic trimer (T2) where the total number of hydrogen bonds is respectively equal to two and three. The theoretical structure factors obtained on the basis of intermolecular arrangements agree fairly well with the experimental one beyond Q = 2 A-1. All through the study, a comparison is made with complementary X-ray results.     

Study of a supramolecular structure of continental type petroleum asphaltenes

Supramolecular, electronic, and chemical structures of petroleum asphaltene molecules are studied. The investigations are carried out by quantum chemistry and molecular mechanics methods. The quantum chemical calculation of the structure-chemical parameters of dimers and trimers of petroleum asphaltenes is made using DFT/B3LYP. The refined values of the ionization potential and electron affinity of petroleum asphaltene molecules, their dimers and trimers agree well with the electron spectroscopy data. The results of the study of geometric structures of petroleum asphaltene dimers and trimers confirm the non-planar structure of asphaltenes.     

Solution structure of the aqueous model peptide N-methylacetamide

Classical molecular dynamics simulations of aqueous N-methylacetamide (NMA) have been performed across a concentration range at 308 K. This peptidic fragment molecule is a useful model for investigating water/peptide hydrogen bond competition. The simulations predict considerable NMA self-association even at low concentrations with a concentration-dependent increase in the ratio of branched to linear clusters. Water-mediated NMA contacts are a feature of this regime, manifested by an unexpected increase in the number of short NMA oxygen contacts arising from water bridge motifs. In contrast, bulk water structure is significantly disrupted by the addition of even small quantities of NMA. With increases in NMA concentration water molecules become progressively more isolated, forming dimers and trimers hydrogen-bonded to NMA. The mixture in this concentration regime may therefore offer a minimal model system for certain structural properties of interior water buried in protein cavities and hydrogen-bonded to mainchain peptide groups.     

Study on hydration enthalpy of N-methylacetamide in water

In order to determine the hydration enthalpy of N-methylacetamide (NMA), the enthalpy change for mixing NMA with liquid water was measured calorimetrically. NMA molecules can self-associate both in the liquid state and in aqueous solutions. The population distribution of the self-associated polymeric species in liquid NMA was evaluated by using the results of ab initio MO calculations for the monomer, dimers, and trimers of trans-NMA, while that in aqueous NMA was obtained by NMR spectroscopy. The relationship between these distributions and the mixing enthalpy was formulated on the basis of the similar energy cycle as Born-Haber type, the schematic diagram of energy cycle is given, and the hydration enthalpy of the NMA monomer was determined accurately. The enthalpy thus obtained was found to be in good agreement with that calculated by ab initio MO theory.     

A computational study of mixed aggregates of chloromethyllithium with lithium dialkylamides

DFT calculations were performed to examine the possible formation of mixed aggregates between chloromethyllithium carbenoids and lithium dimethylamide (LiDMA). In the gas phase mixed aggregates were readily formed and consisted of mixed dimers, mixed trimers, and mixed tetramers. THF solvation disfavored the formation of mixed tetramers and resulted in less exergonic free energies of mixed dimer and mixed trimer formation.     

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.     

Bottom-up assembly of molecular wagons on a surface

The bottom-up assembly of molecular building blocks, carrying specific functions, is a promising strategy for the construction of nanomachines. In this study we show how molecules with a mechanical function, i.e., being equipped with wheels, can be connected in a controlled way directly on a surface. By choosing suitable building blocks, assembled dimers and wagon trains can be formed, whereas the length of the chains can be limited by using a heterogeneous mixture of molecules. By using low temperature scanning tunneling microscopy, the chemical nature of the intermolecular connection is determined as a metal-ligand bond, which is stable enough to maintain the wagon train structure at room temperature. The intermolecular bonds can be controllably changed from trans to cis configurations thereby achieving bond angles of almost 90°.     

Effect of solvent on the cis-trans conformational equilibrium of a proline imide bond of short model peptides in solution.

Proton NMR spectra of proline-containing short peptides with N-terminal sequences of N-acetyl-prolyl- (Ac-Pro-) N-tert-butoxycarbonyl-phenylalanyl-prolyl- (Boc-Phe-Pro-) and N-tert-butoxycarbonyl-leucyl-prolyl- (Boc-Leu-Pro-) were measured in mixed solvents of hexadeuterodimethylsulfoxide and deuterochloroform (CDCl3). Population ratios of cis and trans conformers with respect to the proline imide bond and chemical shifts of NH protons were obtained as a function of a CDCl3 fraction of solvent. With increasing fraction of CDCl3, the trans percentages of the Ac-Pro-imide bonds increased. On the other hand, those of Boc-Phe-Pro- decreased, and those of Boc-Leu-Pro- exhibited middle tendency. From the solvent-dependent variation of the chemical shifts of the NH protons, intramolecular hydrogen bonds that stabilize the trans form of Ac-Pro- and the cis form of Boc-Phe-Pro- were discussed. For the Ac-Pro- peptides, only the trans forms are found to the compatible with 7-, 10-, and 13-membered hydrogen-bonded rings that would be similar to the ordinary secondary structures, gamma- and beta-turns and alpha-helix, respectively. For the cis form of Boc-Phe-Pro-R (R = O-methyl or glycyl-O-ethyl), the hydrogen-bonded structure is found to be similar to the type-VIa beta-turn. On the other hand, for Boc-Phe-Pro-Pro-Leu-Gly-NH2, it has been suggested that two different hydrogen bonds, which are different from that of the type-VIa beta-turn, support each other and cooperatively stabilize the cis form.     

Topology of molecular nanostructures in liquid alcohols

A quantitative topological analysis is conducted of the molecular nanostructures of liquid alcohols as a function of temperature. The analysis is necessary to solve the fundamental problem of the theory of solutions: finding the relationship between the macroparameters of liquids and the structure and properties of intermolecular associates. The analysis is performed using the previously proposed MDGT method, which is based on a combination of molecular dynamics calculations and graph theory. The method enables the recognition and saving of all molecular nanostructures observed in each snapshot of the molecular dynamics trajectory, averaging of data for any number of snapshots to present “averaged” concentrations of associates (dimers, trimers, etc.), and determination of the concentrations and characteristics of isomers (e.g., chains, branched chains, rings, etc.), bond lengths, angles, etc. in each group of associates.     

Photochemical dimerization of acephenanthrylene and the heavy atom effect

The solution-phase photodimerization of acephenanthrylene (1) in cyclohexane, chloroform, dibromomethane, and ethyl iodide with visible light (lambda = 419 nm) occurs to form cis (2) and trans (3) photodimers in ratios that vary with the solvent and with the presence or absence of oxygen. The photodimerization exhibits a significant heavy atom effect and also is sensitive to selective quenching by dissolved oxygen, in which only cis stereoisomers are produced. Irradiation of the dimers (lambda = 254 nm) shows that the trans dimers cleave more rapidly than the cis dimers. This is attributed to stabilization of the excited state in the cis dimers.     

Hydration of simple amides. FTIR spectra of HDO and theoretical studies

The hydration of formamide (F), N-methylformamide (NMF), N,N-dimethylformamide (DMF), acetamide (A), N-methylacetamide (NMA), and N,N-dimethylacetamide (DMA) has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure has been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To facilitate the interpretation of obtained spectral results, DFT calculations of aqueous amide clusters were performed. Molecular dynamics (MD) simulation for the cis and trans forms of NMA was also carried out for the SPC model of water. Infrared spectra reveal that only two to three water molecules from the surrounding of the amides are statistically affected, from among ca. 30 molecules present in the first hydration sphere. The structural-energetic characteristic of these solute-affected water molecules differs only slightly from that in the bulk and corresponds to the clathrate-like hydrogen-bonded cage typical for hydrophobic hydration, with the possible exception of F. MD simulations confirm such organization of water molecules in the first hydration sphere of NMA and indicate a practical lack of orientation and energetic effects beyond this sphere. The geometry of hydrogen-bonded water molecules in the first hydration sphere is very similar to that in the bulk phase, but MD simulations have affirmed subtle differences recognized by the spectral method and enabled their understanding. The spectral data and simulations results are highly compatible. In the case of F, NMF, and A, there is a visible spectral effect of water interactions with N-H groups, which have destabilizing influence on the amides hydration shell. There is no spectral sign of such interaction for NMA as the solute. The energetic stability of water H-bonds in the amide hydration sphere and in the bulk fulfills the order: NMA > DMA > A > NMF > bulk > DMF > F. Microscopic parameters of water organization around the amides obtained from the spectra, which have been used in the hydration model based on volumetric data, confirm the more hydrophobic character of the first three amides in this sequence. The increased stability of the hydration sphere of NMA relative to DMA and of NMF relative to DMF seems to have its origin in different geometries, and so the stability, of water cages containing the amides.     

Configuration of triporphyrin ethers probed by fluorescence measurements.

The fluorescence spectra and lifetimes of triporphyrin ethers derived from hematoporphyrin, mesoporphyrin and protoporphyrin were examined, together with relative hydrophobicities estimated from reverse-phase high performance liquid chromatography (HPLC) elution times. The following data suggest a molecular arrangement with two of the three rings in a "folded configuration". The trimers display a greater fluorescence yield (phi f) than the corresponding diporphyrin ethers which contain only the two folded rings. The fluorescence lifetime data for the trimers are consistent with signals from both a folded ring pair (7-8 ns) and a free ring (14 ns). Reverse-phase HPLC studies indicate that the trimers are intermediate in hydrophobicity between the monomers and dimers. Preliminary data suggest that, for certain peripheral substitutions, the trimer configuration is superior to the dimer for photodynamic therapy.     

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.     

Asymmetric allyl-metal bonding in substituted (eta3-allyl) palladium complexes: X-ray structures of cis- and trans-4-acetoxy-

Enantiomerically pure cis and trans isomers of 4-acetoxy-[eta3(1,2,3)-cyclohexenyl]palladium chloride dimers (cis-1 and trans-1) were prepared from enantiomerically pure trans-1-acetoxy-4-chloro-2-cyclohexene. X-ray analyses of these complexes show that in the trans complex (trans-1) the six-membered ring prefers a chair conformation, whereas in the cis complex (cis-1) the cyclohexenyl ring has a boat conformation. According to the X-ray structure of trans-1 the Pd-C3 bond is shorter than the other allylic terminal palladium-carbon bond (Pd-C1). On the other hand, in cis-1 the Pd-C3 and Pd-C1 bond lengths are identical within the experimental error. The calculated structures (B3PW91/LANL2DZ + P) of trans-1 and cis-1 also display differences in the allylpalladium bonding. The asymmetric allylpalladium bonding in trans-1 is explained on the basis of pi-sigma electronic interactions between the 4-acetoxy substituent and the allyl-metal moiety.     

Pyridyl 'ring-flipping' in the dimers [Me2E(2-py)]2 (E=B, Al, Ga; 2-py=2-pyridyl)

The boron and aluminium dimers [Me2E(micro-py)]2 [E=B (1); Al (2)] are formed as mixtures of two isomers in which the group 13 centres are coordinated by the bridging 2-py ligands in a cis or trans manner, however, in contrast to previous studies, we find that simply heating the mixtures of these isomers of and gives the more thermodynamically stable (synthetically useful) trans isomers exclusively (the trans isomer being the only product in the case of the gallium analogue ).     

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.     

Dimeric aluminum-phosphorus compounds as masked frustrated Lewis pairs for small molecule activation

Hydroalumination of aryldialkynylphosphines RP(C≡C-(t)Bu)(2) (R = Ph, Mes) with equimolar quantities of diethylaluminum hydride afforded mixed alkenyl-alkynyl cyclic dimers in which the dative aluminum-phosphorus bonds are geminal to the exocyclic alkenyl groups. Addition of triethylaluminum to isolated 1 (R = Ph) or to the in situ generated species (R = Mes) caused diethylaluminum ethynide elimination to yield the arylethylphosphorus dimers 2 and 3. These possess a chair-like Al(2)C(2)P(2) heterocycle with intermolecular Al-P interactions. The boat conformation (4) was obtained by the reaction of (t)Bu-P(C≡C-(t)Bu)(2) with di(tert-butyl)aluminum hydride. Despite being dimeric, 2 behaves as a frustrated Lewis pair and activates small molecules. The reaction with carbon dioxide gave cis/trans isomeric AlPC(2)O heterocycles that differ only by the configuration of the exocyclic alkenyl unit. Four isomers resulted from the reaction with phenyl isocyanate. This is caused by cis/trans isomerization of the initial C=O adduct and subsequent rearrangement to the AlPC(2)N heterocycle, being the C=N adduct.     

Three- and four-center trans effects in triply bonded ditungsten complexes: an ab initio molecular dynamics study of compounds with stoichiometry W2Cl4(NHEt)2(PMe3)2

We have performed ab initio molecular dynamics simulations based on density functional theory to characterize the structural, electronic, and dynamic properties of the three major isomeric forms of the title compound. In agreement with experimental results, calculations with two different parametrizations of the exchange-correlation functional (BLYP and BP) both indicate the cis-C2 form as the most stable isomer. The relative energies of the different forms are, however, small (less than approximately 1-2 kcal/mol), and the three compounds show overall very similar ground-state properties. Larger differences exist in their finite temperature behavior, which is dominated by the facile dissociation of one or both phosphine ligands. The calculated activation energies for phosphine dissociation differ clearly for the trans and the cis isomers and vary in the order trans < cis-C2 less than approximately cis-Ci. Analysis of the electronic structure of the transition states shows that the difference in activation energy between cis and trans isomers can be rationalized in terms of a classic trans effect caused by a molecular orbital spanning the three atomic centers N-W-P. The subtle difference between the two cis isomers, on the other hand, is likely due to an analogous four-center trans effect N-W-W-P which is mediated via metal-metal orbitals and involves ligands on both tungsten atoms.     

Conformational analysis. 24. Structure and composition of gaseous oxalyl fluoride, C(2)F(2)O(2): electron-diffraction investigation augmented by data from microwave spectroscopy and molecular orbital calculations

The molecular structure and composition of gaseous oxalyl fluoride (OXF) has been investigated by electron diffraction (GED) at nozzle-tip temperatures of -10, 149, and 219 degrees C. The GED data were augmented by molecular orbital calculations, and the analysis was aided by use of rotational constants from microwave (MW) spectroscopy. As in the other oxalyl halides, there are two stable species, of which the more stable is periplanar anti (i.e., trans). However, unlike these other halides in which the second form is gauche, the second form of oxalyl fluoride was known from MW work to be periplanar syn (i.e., cis). Our results are consistent with a mixture of trans and cis forms, and yield values for the structural parameters, the composition of the system at the three temperatures cited, and the thermodynamic quantities deltaG(o), deltaH(o), and deltaS(o) for the reaction trans --> cis. Some trans/cis distances (r(g)/Angstrom) and angles (<(alpha)/deg) at -10 degrees C are r(C=O) = 1.178(2)/1.176(2), r(C-F) = 1.323(2)/1.328(2); r(C-C) = 1.533(3)/1.535(3), <(C-C=O) = 126.4(2)/124.2(2), <(C-C-F) = 109.8(2)/112.2(2), and <(O-C-F) = 123.8(2)/123.6(2). The mixture compositions (percent trans) at -10 degrees C/149 degrees C/219 degrees C are 75(3)/58(7)/52(8), from which deltaH(o) and deltaSO) are found to be 1.14 kcal/mol and 2.12 cal/(mol x deg). The system properties are discussed.