X-ray crystal structure analyses and atomic charges of color former and developer. I. Color developers

The crystal and molecular structures of 2,2-bis(4-hydroxyphenyl)propane (Bisphenol A, BPA) (1), benzyl 4-hydroxybenzoate (2), 1,7-bis(4-hydroxyphenylthio)-3,5-dioxaheptane (3) and 4-hydroxyphenyl 4-isopropoxyphenyl sulfone (4) have been determined by X-ray crystal structure analysis. Theoretical calculations of the steric hindrance and semiempirical quantum chemical calculations to determine the color characteristics have been carried out. It is clear that the energy barriers for the variation of the orientation of phenol group in 1 to 4 are due to steric hindrance caused by the other moiety and the peak profiles are due to repulsive interactions of the other moiety. Net atomic charges on the hydrogen of the OH group are larger than those on the other atoms in the molecules. This high electron charge of the para orientation will cause the different thermosensitivity and stabilization.     

X-ray crystal structure analysis and atomic charges of color former and developer: 2. Color formers

The crystal and molecular structures of 2′-amino-6′-dibutylamino-3′-methylspiro[isobenzofuran-1(3H), 9′[9H]xanthen]-3-one (1), 2′-amino-6′-(N-cyclohexyl-N-methylamino)-3′-methylspiro[isobenzofuran-1(3H), 9′[9H]xanthen]-3-one (2) and 2′-(2-chlorophenyl)amino-6′-dibutylaminospiro[isobenzofuran-1(3H), 9′[9H]xanthen-3-one (3) have been determined by single-crystal X-ray diffraction analysis. Atom-atom non-bonded potential energy and semiempirical quantum chemical calculations have been performed. The xanthene rings of 1 to 3 are slightly bent and the phthalide rings are planar. The phthalide ring moieties are almost perpendicular (88.9(1)–93.5(5)°) to the xanthene rings. The bond lengths C(6)---O(2) are apparently extended from the normal C(sp³---O (lactone) length. The temperature factors for one butyl group C(32)---C(35)) of 1 increase gradually toward the terminal carbon. The temperature factors for C(30)---C(33) of 2 indicate large vibrations and these are reflected in short bond lengths. Two butyl groups of 3 are disordered and these C---C bond lengths are short and long alternately. Atomic net charges around spirocarbon C(6) and toward N(1) to C(6) indicate the weak alternative system in the colorless form. As the xanthene ring has a planar geometry, the π electron density migration will easily occur from the auxochromes attached to the phthalide ring to the xanthene ring.     

X-ray crystal structure analysis and atomic charges of color former and developer: 2. Color formers

The crystal and molecular structures of 2′-amino-6′-dibutylamino-3′-methylspiro[isobenzofuran-1(3H), 9′[9H]xanthen]-3-one (1), 2′-amino-6′-(N-cyclohexyl-N-methylamino)-3′-methylspiro[isobenzofuran-1(3H), 9′[9H]xanthen]-3-one (2) and 2′-(2-chlorophenyl)amino-6′-dibutylaminospiro[isobenzofuran-1(3H), 9′[9H]xanthen-3-one (3) have been determined by single-crystal X-ray diffraction analysis. Atom-atom non-bonded potential energy and semiempirical quantum chemical calculations have been performed. The xanthene rings of 1 to 3 are slightly bent and the phthalide rings are planar. The phthalide ring moieties are almost perpendicular (88.9(1)−93.5(5)°) to the xanthene rings. The bond lengths C(6)---O(2) are apparently extended from the normal C(sp³)---O (lactone) length. The temperature factors for one butyl group C(32)---C(35)) of 1 increase gradually toward the terminal carbon. The temperature factors for C(30)---C(33) of 2 indicate large vibrations and these are reflected in short bond lengths. Two butyl groups of 3 are disordered and these C---C bond lengths are short and long alternately. Atomic net charges around spirocarbon C(6) and toward N(1) to C(6) indicate the weak alternative system in the colorless form. As the xanthene ring has a planar geometry, the π electron density migration will easily occur from the auxochromes attached to the phthalide ring to the xanthene ring.     

X-ray crystal structure analysis and atomic charges of color former and developer: 5. Colored formers

The spirocarbon C6 of colorless forms of a fluoran compound is the base of the disengagement from the bond C(sp³)–O by the accessibility of the electrophilic H⁺, the phthalide ring is cleaved and this ring becomes a benzene ring D and a carboxyl group as colored forms. The crystal and molecular structures of colored forms 2-anilino-3-methyl-6-diethylamino-9-(o-carboxyphenyl) xanthene C₃₁H₂₉N₂O₃⁺·Cl⁻ (1) and 2-methyl-3-anilino-7-dibutylamino-9-(o-carboxyphenyl) xanthene C₃₅H₃₇N₂O₃⁺·Cl⁻ (2) complexes were determined by single-crystal X-ray diffraction analysis. The xanthene ring skeletons of colored forms 1 and 2 have planar geometries, and the ring junctions between the xanthene ring and the benzene ring D make a small angle compared to the colorless forms which are almost at right angles to the xanthene ring skeletons. 1 and 2 are just different from the ethyl and butyl groups in two side chains R¹ and R², but the rigid body and internal motions in molecules differ at R¹ and R⁵ (the ring F). The charges of the root atom N1 of the two side chains are increased by π-electron densities, those from N1 to C6 atoms show distinct odd alternant system, and two oxygens (O2 and O3) of the carboxyl group are decreased. The group charges of N1 of colored forms are positive, while those of the colorless forms are negative. Colored forms make networks of X–HY contacts with an anion Cl⁻ and the anion in the nucleus of network. It is explained here that delicate positive charges of atoms N2 and O2 cause ClH(N2)–N2 and ClH(O2)–O2 contacts.     

A convenient synthesis and crystal structure of disubstituted 1,2,3-triazoles having ether functionality

Abstract

A series of 27 ether-linked 1,4-disubstituted 1,2,3-triazoles (8a–8z₁) has been synthesized by 1,3 dipolar cycloaddition of 1-substituted-4-(prop-2-yn-1-yloxy)benzene (3a–3c) and aromatic azides (5a–5c, 7a–7f). The synthesized compounds were explicated by FTIR, ¹H NMR, ¹³C NMR and HRMS techniques. The structures of synthesized triazoles 8c (CCDC 1840219) and 8f (CCDC 1840220) were also confirmed by X-ray crystallography.     

Native surface structure of natural soil particles determined by combining atomic force microscopy and X-ray photoelectron spectroscopy

A procedure was developed for handling natural soil particles and probing their native surface structure by atomic force microscopy (AFM) under water. This procedure was used to investigate the nanometer scale organisation of organic matter at the surface of sand particles taken from three soil horizons. The latter were selected for the contrasted properties of their organic matter, namely Podzol E and Bh horizons and a Cambisol A–B horizon. The presence of an adsorbed layer was visualised at the surface of Podzol Bh and Cambisol particles in the form of aggregated structures that interacted with the AFM probe. Surface analysis by X-ray photoelectron spectrometry (XPS) confirmed the carbonaceous nature of this adsorbed layer. Displacement of organic matter by the scanning probe was directly evidenced for Podzol Bh sand particles. Such displacement was not observed for Cambisol particles. A dramatic effect of drying on the concentration, nanometer scale distribution and properties of the adsorbed organic matter was clearly demonstrated by combining AFM imaging and XPS analysis. The procedure developed here gives access to direct, nanoscale information of the surface structure of sand particles and offers promising prospects for the characterisation of other environmentally-relevant particles in native conditions.     

The crystal structure of 1-p-bromophenylsilatrane at 293 K and 133 K

The crystal structure of 1-p-bromophenylsilatrane was determined at ambient and low temperature. The methylene groups of the silatrane skeleton in the β-position to the nitrogen atom are disordered in the ambient temperature structure. The disorder disappears at 133 K. The Si ← N dative bond length is nearly identical at both temperatures (2.139(3) and 2.132(2) Å). The deviation of the atoms in the silatrane moiety from the ideal three-fold symmetry seems to point to the most dynamically behaving parts of the molecule.     

Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites,solvent density,and solvent dipole

The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.     

Accurate molecular electrostatic potentials based on modified PRDDO/M wave functions. I. Electrostatic potential derived atomic charges

A new approach for the calculation of electrostatic potential derived atomic charges is presented. Based on molecular orbital calculations in the PRDDO/M approximation, the new parametrized electrostatic potential (PESP) method is parametrized against ab initio MP2/6-31G** calculations. For a data set of 820 atoms in 145 molecules containing H, C, N. O, F, P, S, Cl, and Br (including hypervalent species), the PESP method achieves a mean absolute error of 0.037 e⁻ with a correlation coefficient of 0.990. Unlike other approximate approaches, no scaling factor is required to improve the agreement between PESP charges and the underlying ab initio results. PESP calculations are an order of magnitude faster than the simplest ab initio calculation (STO-3G) on large molecules while achieving a level of accuracy that rivals much more elaborate ab initio methods. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 955–969, 1997     

Synthesis of platinum-iodo-alkyl/aryl complexes in ligand-exchange reactions: Determination of the structure of Pt{(S,S)-bdpp}(X)I complexes (X = Me, I) by X-ray crystallography

Pt{(S,S)-bdpp}(R)I (bdpp = 2,4-bis(diphenylphosphino)pentane; R = Me, Ph, Bz, 2-Tioph) complexes were formed in alkyl/aryl ligand - iodide ligand-exchange reactions by reacting the corresponding Pt{(S,S)-bdpp}R₂ complexes with methyl iodide. The Pt{(S,S)-bdpp}(Me)I complex was isolated and fully characterised. The influence of the X ligand on the platinum-bdpp chelate conformation was investigated in Pt{(S,S)-bdpp}(X)I (X = I, SnCl₃, Me) complex series by means of X-ray crystallography.     

The crystal structure of 3-methyluracil from X-ray powder diffraction data

The crystal structure of 3-methyluracil has been determined ab initio by conventional monochromatic X-ray powder diffraction data. The crystal data are: orthorombic, a=6.6294(1), b=13.1816(3), c=6.53938(9) (Å), V=571.45(3) (ų), space group Pbnm, Z=8. The structure was solved by direct methods and the final Rietveld refinement converged to R_p=0.0398, R_wp=0.0528, R_Bragg=0.0294. The crystal structure exhibits endless chains of planar molecules, connected via head-to-tail N-H?O hydrogen bonds.     

Two new phosphinic amides: Synthesis,crystal structure,and theoretical study of hydrogen bonding

Two novel phosphinic amides, (C₆H₅)₂P(O)(NH?cyclo?C₇H₁₃) (I) and (C₆H₅)₂P(O)(NH?cyclo?C₆H₁₁) (II) were synthesized and characterized by spectroscopic methods and X-ray crystallography. Both compounds crystallize in the orthorhombic chiral space group P2₁2₁2₁ and in both structures, the N—H···O hydrogen bonds lead to one-dimensional arrangements along the a axis. The molecular geometries and vibrational frequencies of I and II were investigated with quantum chemical calculations at the B3LYP/6–311G^** level of theory. Furthermore, the hydrogen bonds were studied by means of the Bader theory of atoms in molecules (AIM) and natural bond orbital (NBO) analysis.     

Synthesis of a new 24-membered tetramide macrocycle and X-ray crystal structure determination

The synthesis and characterization of a new 24-membered tetramide macrocycle (6) related to Leigh's macrocycles and catenanes is reported. The replacement of p-xylylenediamine (Leigh) by m-xylylenediamine (this work) strongly modifies the geometry and properties of the new macrocycle. NMR spectroscopy (in DMSO?d₆ solution) and X-ray crystallography have been used to characterize compound 6. The structural features in the crystal (conformational aspects and H-bonding) have been discussed comparatively to two similar macrocycles NEWHIJ and UJUNOC.     

Fast,efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method

The AM1‐BCC method quickly and efficiently generates high‐quality atomic charges for use in condensed‐phase simulations. The underlying features of the electron distribution including formal charge and delocalization are first captured by AM1 atomic charges for the individual molecule. Bond charge corrections (BCCs), which have been parameterized against the HF/6‐31G* electrostatic potential (ESP) of a training set of compounds containing relevant functional groups, are then added using a formalism identical to the consensus BCI (bond charge increment) approach. As a proof of the concept, we fit BCCs simultaneously to 45 compounds including O‐, N‐, and S‐containing functionalities, aromatics, and heteroaromatics, using only 41 BCC parameters. AM1‐BCC yields charge sets of comparable quality to HF/6‐31G* ESP‐derived charges in a fraction of the time while reducing instabilities in the atomic charges compared to direct ESP‐fit methods. We then apply the BCC parameters to a small “test set” consisting of aspirin, d ‐glucose, and eryodictyol; the AM1‐BCC model again provides atomic charges of quality comparable with HF/6‐31G* RESP charges, as judged by an increase of only 0.01 to 0.02 atomic units in the root‐mean‐square (RMS) error in ESP. Based on these encouraging results, we intend to parameterize the AM1‐BCC model to provide a consistent charge model for any organic or biological molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 132–146, 2000     

Analysis of atomic displacement parameters and molecular motion in crystals. Part 2. X-ray crystal structure of K2Ru(SO4)2 * 6H2O at 160 K and 295 K

Atomic displacement parameters determined from a single-crystal X-ray-diffraction study on K₂Ru(SO₄)₂ * 6H₂O are analyzed in the molecular mean field approximation. The motion of SO₂ ^2– can be described with a rigid-body model, whereas for [Ru(H₂O)₆]²⁺ internal stretching motion and coupling between stretching motion and overall translation are found to be necessary for explaining the observed atomic displacement parameters. Frequencies and force constants of internal motion are not significantly affected by such couplings. K₂Ru(SO₄)₂ * 6H₂O crystallizes in the monoclinic space groupP2₁/c (No. 14), witha = 6.1211(7)Å,b = 12.226(2) Å,c = 8.916(2)Å, = 105.11(1)°,Z = 2 at 160 K anda = 6.1402(7)Å,b = 12.274(2)Å,c = 8.957(1)Å, = 105.25(1)°,Z = 2 at 295 K. The structure was refined to a finalR(F) of 0.017 at 160 K and of 0.019 at 295 K for 1438 and 1299 observed reflections withF ₀ > 6(F₀) and sin / > 0.617 Å^1–.     

One-pot facile synthesis,crystal structure and antifungal activity of 1,2,3-triazoles bridged with amine-amide functionalities

A library of twenty five 1,2,3-triazoles bridged with amine-amide functionalities have been synthesized from reaction of N-substituted(prop-2-yn-1-yl)amines (2a–2e), 2-bromo-N-arylacetamides (4a–4e) and sodium azide through copper(I)-catalyzed alkyne-azide cycloaddition. The synthesized compounds were characterized by using FTIR, ¹H NMR, ¹³C NMR, and HRMS techniques. The structures of synthesized 5a (CCDC 1569245) and 5h (CCDC 1569249) were also confirmed by X-ray crystallography. Antifungal evaluation of newly synthesized triazoles was carried out against – Candida albicans and Aspergillus niger. Biological screening of synthesized 1,2,3-triazoles revealed moderate to good antifungal activity against tested strains.     

X-ray crystal structure of a p-hydroxycalix[6]arene derivative

The first molecular structure of a p-hydroxycalix[6]arene 6 has been determined by a single crystal X-ray diffraction study. The calix[6]arene molecule assumes a 1,2,3-alternate conformation with all OH groups at the upper rim engaged in H-bonds with pyridine molecules. The stacking of molecules of p-hydroxycalix[6]arene 6 along the a and c axes gives rise to a solvent pseudo-cylindrical cavity at the centre of the cell.     

X射线晶体学和电子晶体学在分子筛结构表征中的应用

分子筛是一类具有规则孔道或笼结构的晶态微孔材料, 在吸附、 分离和催化中都表现出了优异的性能. 为了探索其结构与性质的关系, 在原子尺度上研究分子筛的微观结构是十分必要的. 本综述介绍了一系列与X射线晶体学和电子晶体学相关的表征技术（倒易空间和正空间）在分子筛结构表征中的应用. 随后, 基于分子筛的结构表征方法和化学组成, 对2007年之后发现的85种新分子筛进行了系统总结, 对其中9种具有独特合成方法或结构特征的分子筛进行了详细介绍.