Vibrational spectra of 1,1,3,3-tetramethyl-2-nitroguanidine and their interpretation with the use of scaling of quantum-chemical force field

The IR (4000–50 cm⁻¹) and Raman (3500–170 cm⁻¹) spectra of solid 1,1,3,3-tetramethyl-2-nitroguanidine (TMNG) were obtained. The spectra were interpreted using the scaling of the TMNG quantum-chemical force field in the B3LYP/6-311G(d,p) approximation. Transferable scale factors necessary for the interpretation of spectra of more complex related compounds were determined. The scaled harmonic force field is supposed to be used in the analysis of the available gas-phase electron diffraction data for TMNG. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 495–498, March, 2008.     

Molecular structure of p-diisocyanobenzene from gas-phase electron diffraction and theoretical calculations and effects of intermolecular interactions in the crystal on the benzene ring geometry

In this study, the molecular structure of p-diisocyanobenzene has been determined by gas-phase electron diffraction and quantum chemical calculations. The electron diffraction intensities from a previous study by Colapietro et al. (J Mol Struct 125:19–32, 1984) have been reanalyzed using geometrical constraints and initial values of vibrational amplitudes from computations. The equilibrium structure of the molecule has D _2h symmetry, whereas the average geometry in the gaseous phase is best described by a non-planar model of C _2v symmetry. The lowering of symmetry is due to large-amplitude motion of the substituents out of the plane of the benzene ring. The non-planar model has an internal ring angle at the ipso position, ∠_aC2–C1–C6 = 120.6 ± 0.2°, about 1° smaller than that from the previous study, but consistent with the quantum chemical calculations. The mean length of the ring C–C bonds and the length of the triple bond are accurately determined as 〈r _g(C–C)〉 = 1.398 ± 0.003 Å and r _g(N≡C) = 1.177 ± 0.002 Å, respectively. Comparison with the gaseous isoelectronic molecules p-diethynylbenzene and p-dicyanobenzene shows that the differences in the mean lengths of the ring C–C bonds and in the lengths of the triple bonds determined by electron diffraction are equal or closely similar to the corresponding differences from quantum chemical calculations. The present experimental value of the ipso angle in free p-diisocyanobenzene is slightly, but significantly smaller than that obtained by X-ray crystallography. The difference is confirmed by computational modeling of the crystal structure and appears to be due to –N≡C···H–C intermolecular interactions in the crystal.     

The geometry of intermolecular interactions in some crystalline fluorine-containing organic compounds

The propensity of C-F groups to form C-F H-C interactions with C-H groups on other molecules has been analyzed. Crystal structures of molecules containing only carbon, hydrogen, and fluorine, but no oxygen, nitrogen, or other hydrogen-bond-forming elements, were chosen for an initial study in which the intermolecular interactions in crystal-structure determinations of polycyclic aromatic hydrocarbons and their analogous fluoro derivatives were analyzed. It is found that C-F H-C interactions occur, but they are weak, as judged by the intermolecular distances and the angles involved. In a study of crystal structures of molecules containing other elements in addition to carbon, hydrogen, and fluorine, it was found that when an oxygen atom is in a neighboring position on an interacting molecule, a C-O group is more likely than a C-F group to form a linear interaction to the hydrogen atom of a C-H group. Thus, in spite of the high electronegativity of the fluorine atom, a C-F group competes unfavorably with a C-O^–, C-OH, or C=O group to form a hydrogen bond to an O-H, N-H, or C-H group. It is found, however, particularly for polycyclic aromatic hydrocarbons with substituted CF₃ groups that, in the absence of other functional groups that can form stronger interactions, C-F H-C interactions may serve to align molecules and give a different crystal packing from that in the pure hydrocarbon (where fluorine is replaced by hydrogen). Thus, C-F H-X (X = C, N, O) interactions are very weak, much weaker than C=O H-X interactions, but they cannot be ignored in predictions of modes of molecular packing in complexes and in crystals.     

Neutron diffraction evidence for substrate-triggered intermolecular interactions in the ribosomal protein IF-2

Small-angle neutron scattering experiments provide evidence for substrate-triggered intermolecular correlations between ribosomal protein molecules. The long-range interactions, very likely electrostatic in nature are postulated to be of biological relevance in the transmission of the genetic message.     

Stereoelectronic interactions in the fragment N-C-CN from high-resolution X-ray diffraction data and quantum chemical computations

Analysis of the experimental electron density distribution function for the crystal and quantum chemical calculations revealed some distinctive features of stereoelectronic interactions (SI) in the fragment N-C-CN. The SI-induced changes in the atomic parameters were characterized in terms of the “Atoms in Molecules” theory. These interactions were compared with competitive SI in the fragment N-C-N. The crystal packing in organic cyanides is discussed. According to the data obtained, relatively weak SI in the fragment N-C-CN can be decisive for the molecular conformation in the crystal when there are no strong competitive interactions.     

Conformational analysis of the methyl ester of alanine by gas electron diffraction and Ab initio geometry optimization

The gas electron diffraction data of the methyl ester of -alanine were recorded at an approximate nozzle temperature of 80°C and analyzed with geometrical constraints taken from 4-21G ab initio gradient geometry refinements. The molecular intensities are consistent with a model for the most populated conformational state in which the N---C---C=O torsion (τ) is syn-peri-planar and a bifurcated hydrogen bond exists between NH₂ and C=O. Details of the intensity data make it impossible to rule out the presence of significant concentrations of a second conformer, (τ + 150°), in contrast to the ab initio calculations which predict greater stability of the system at τ −150° than +150°.     

The molecular structure of tetramethoxymethane in the gas phase: an electron diffraction study

The electron diffraction study of tetramethoxymethane showed that in the gas phase the molecule has S₄ symmetry, flattened along the S₄ axis. Central and peripheral C-O bond lengths are different, consistent with considerations based on the anomeric effect. Comparison is made with ab initio calculations on methanediol. The geometrical parameters (r_g(1) structure) are: central C-O bond 1.395 Å; peripheral C-O bond 1.422 Å; C-H bond 1.11 Å; O-C-O angle bisected by the S₄. axis 114.7°; C-O-C angle 114.0°; O-C-H angle 111.9°; methoxy torsional angle 63.1°; methyl torsional angle 48.5°.     

Structure of new derivatives of perhydropyrimidine-2-ones and intermolecular interactions in their crystals

Six new derivatives of perhydropyrimidine-2-ones obtained in a three-component system of urea, aromatic aldehydes, and dichloromethylacetylbenzoylmethanes are studied by single crystal X-ray diffraction. The molecules have three chiral centers, but out of four possible diastereomeric pairs for each of the compounds, crystals of only one diastereomer are obtained. Moreover, four of them crystallize as true racemates, and two as racemic conglomerates. Crystals of five compounds are solvates with solvents of different nature (water, acetonitrile, dimethylformamide, dimethylsulfoxide). Crystals of the compounds are stabilized by both classical hydrogen bonds of N–H?O and O–H?O types and interactions of the С–H?O type.     

The structure of 1,3-dichloropropyne as determined by gas electron diffraction and comparison with microwave data

The structure of 1,3-dichloropropyne has been studied by gas electron diffraction. The resulting parameters r_a have been converted into r_α^o distances. A geometrical structure has been fitted to these internuclear distances. Thus the following parameters (r_α^o) have been determined: r(C₁-Cl₁) = 1.629 (10) A, r(C₁C₂) = 1.201 (13) Å, r(C₃-Cl₂) = 1.791 (6) A, ∠(C₂-C₃-Cl₂) = 111.1° (1.0°), ∠(H-C₃-H) = 98.8° (3.1°), ∠(C₂-C₃-H) = 108.7° (3.2°). ∠(Cl₁-C₁C₂) = 176.6° (1.1°), ∠(C₁C₂-C₃) = 182.7° (1.4°). Inconsistencies have been detected between our results and the rotational constants reported by Günther and Zeil. Discussion of the problem including rotational constants of the first excited vibrational state leads to the conclusion that the observed discrepancies are due to temperature effects.     

Thermal dissociation of protein-oligosaccharide complexes in the gas phase: mapping the intrinsic intermolecular interactions

Blackbody infrared radiative dissociation (BIRD) and functional group replacement are used to map the location and strength of hydrogen bonds between an antibody single chain fragment (scFv) and its natural trisaccharide receptor, alpha-D-Galp (1-->2)[alpha-D-Abep (1-->3)]alpha-D-Manp1-->OMe (1), in the gaseous, multiply protonated complex. Arrhenius activation parameters (E(a) and A) are reported for the loss of 1 and a series of monodeoxy trisaccharide congeners (5-8 identical with tri) from the (scFv + tri + 10H)(+10) complex. The energetic contribution of the specific oligosaccharide OH groups to the stability of the (scFv + 1 + 10H)(+10) complex is determined from the differences in E(a) measured for the trisaccharide analogues and 1 (55.2 kcal/mol). A decrease of 6 to 11 kcal/mol in E(a), measured for the monodeoxy trisaccharides, indicates that the deleted OH groups interact strongly with the scFv and that they account for a majority of the stabilizing intermolecular interactions. A partial map of the hydrogen bond donor/acceptor groups of 1 and the strength of the interactions is presented for the protonated +10 complex. A comparison of the gas-phase map with the crystal structure indicates that significant structural differences exist. The hydroxyl groups located outside of the binding pocket, and exposed to solvent in solution, participate in new protein-oligosaccharide hydrogen bonds in the gas phase. The decrease in kinetic and energetic stability of the (scFv + 2 + nH)(n)()(+) complex with increasing charge-state is attributed to conformational differences in the binding region induced by electrostatic repulsion. The similarity in the Arrhenius parameters for the +9 and +10 charge states suggests that repulsion effects on the structure of the binding region are negligible below +11.     

Modeling of scattering on the residual gas in an electron diffraction experiment

The scattering on the residual gas in an electron diffraction chamber is modeled. A comparison with experimental data reveals that is this scattering that may make a major contribution to the extraneous signal inevitably present in the recorded diffraction pattern. Practical recommendations on the development of the electron diffraction apparatus design are given.     

The effect of finite scattering geometry on measured electron diffraction cross sections: Part II. Structural parameters

Model calculations of averaged electron diffraction cross sections were employed to determine if and when the finite scattering geometry affects molecular structure parameters derived from 40 ke V electrons scattered on CO₂, CF₄ and C₆H₆. No appreciable change in the index of resolution and the internuclear distance was found. Although the mean amplitudes of vibration change noticeably, the results indicate that the scattering geometry cannot account for the discrepancies between those determined from electron diffraction data and those derived from spectral results.     

高能体系分子间相互作用研究: 含NNO~2和NH~2混合物

以abinitioHF/6-31G^*计算求得NH~3+NH~2NO~2的两种优化构型,经MP4电子相关能校正和Boys-Bernardi方案校正基组叠加误差求得精确的分子间相互作用能。还用PM3方法计算研究TATB(均三氨基三硝基苯)分别与HMX(奥克托金)和RDX(黑索金)的混合体系,经色散能校正电子相关近似地求得分子间相互作用能。结果表明,NH~3与NH~2NO~2之间的最大结合能为-38.32kJ/mol;分子间相互作用增强了N-NO~2键强度;TATB与HMX,RDX的结合能远大于石墨与HMX或RDX的结合能,表明TATB对HMX和RDX的润湿和钝感作用较石墨更强。     

The molecular structure of tetramethoxysilane in the gas phase,an electron diffraction study

The molecular structure of tetramethoxysilane was determined in the gas phase by electron diffraction. The molecule has S₄ symmetry, slightly flattened along the axis. The SiO bonds are shorter than in methylsilylether, demonstrating the effect of electronegative substituents on the Si atom. The geometrical parameters (r_a structure) are: Si-O bond 1.613 Å; C-O bond 1.414 Å; C-H bond 1.12 Å; O-Si-O angle bisected by S₄ axis 115.5°; Si-O-C angle 122.3°; O-C-H angle 111°; methoxyl torsional angle 64°; methyl torsional angle 60°.