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1.
The molecular configuration and crystal structure of solid polycrystalline N,N′′‐diacetylbiuret (DAB), a potential nitrogen‐rich fertilizer, have been analyzed by a combination of solid‐ and liquid‐state NMR spectroscopy, X‐ray diffraction, and DFT calculations. Initially a pure NMR study (“NMR crystallography”) was performed as available single crystals of DAB were not suitable for X‐ray diffraction. Solid‐state 13C NMR spectra revealed the unexpected existence of two polymorphic modifications (α‐ and β‐DAB) obtained from different chemical procedures. Several NMR techniques were applied for a thorough characterization of the molecular system, revealing chemical shift anisotropy (CSA) tensors of selected nuclei in the solid state, chemical shifts in the liquid state, and molecular dynamics in the solid state. Dynamic NMR spectroscopy of DAB in solution revealed exchange between two different configurations, which raised the question, is there a correlation between the two different configurations found in solution and the two polymorphic modifications found in the solid state? By using this knowledge, a new crystallization protocol was devised which led to the growth of single crystals suitable for X‐ray diffraction. The X‐ray data showed that the same symmetric configuration is present in both polymorphic modifications, but the packing patterns in the crystals are different. In both cases hydrogen bonds lead to the formation of planes of DAB molecules. Additional symmetry elements, a two‐fold screw in the case of α‐DAB and a c‐glide plane in the case of β‐DAB, lead to a more symmetric (α‐DAB) or asymmetric (β‐DAB) intermolecular hydrogen‐bonding pattern for each molecule.  相似文献   

2.
A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946-950) on the Asp 25-Asp25' dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26-36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637-9642).  相似文献   

3.
Major antioxidants of aqueous ethanol extract from Lady's Finger (Hibiscus esculentus Linn) were systematically investigated in this study. Firstly, high-performance liquid chromatography (HPLC) was applied to identify antioxidant peaks in a sample by spiking the sample extract with 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) free radical, which was prepared from manganese dioxide and ABTS. Secondly, in order to identify the elution period of major antioxidant peaks, the antioxidant capacities of different fractions from solid-phase extraction (SPE) were measured, and the chromatograms of fractions were also recorded. Lastly, multiple mass spectrometry (MS(n)) was used to elucidate the possible chemical structures of antioxidants, and nuclear magnetic resonance (NMR) was further applied for structure confirmation. The major antioxidant compounds in lady's finger were identified to be quercetin derivatives and (-)-epigallocatechin using HPLC-MS and HPLC-MS(n) (n = 2-4) techniques. It was found that about 70% of total antioxidant activity was contributed by four quercetin derivatives. The structures of major antioxidants, which were isolated by semi-preparative RP-HPLC with two tandem C18 columns, were further confirmed using UV-vis absorption spectroscopy and 13C NMR spectra. Quercetin 3-O-xylosyl (1' --> 2') glucoside, quercetin 3-O-glucosyl (1' --> 6') glucoside, quercetin 3-O-glucoside and quercetin 3-O-(6'-O-malonyl)-glucoside were first identified and characterized as major antioxidants in lady's finger.  相似文献   

4.
The conformational properties of monosaccharides constitute fundamental features of oligosaccharides. While the energy landscape of monosaccharides can be altered by a specific biochemical environment or by chemical modifications, the analysis of resulting dynamic conformational equilibria is not feasible by experimental means alone. In this work, a series of β-d -xylopyranosides is used to outline how a combination of experimental NMR parameters and computed molecular properties can be used to determine conformers and quantify the composition of conformational equilibria. We demonstrate that identifying the most stable conformers using energy calculations is challenging and computing of NMR shieldings is typically not sensitive enough. On the other hand, computed spin-spin coupling constants for the xyloside ring can be used to unambiguously assign experimental NMR data of dynamic conformational equilibria and quantify the ratio of different conformers in the mixture. As a proof of principle, this procedure allowed to analyze a hitherto unknown dynamic equilibrium of a diamino-xyloside as a precursor of a molecular switch.  相似文献   

5.
Benzo-condensed dithieno[3,2-b:2',3'-d]phospholes have been synthesized that allow convenient tuning of properties that are essential for application as semiconductor materials in organic field-effect transistor (OFET) devices. The versatile reactivity of the trivalent phosphorus atom in these heteropentacenes provides access to a series of materials that show different photophysical properties, significantly different organization in the solid state, and distinctly different electrochemical properties that can be achieved by simple chemical modifications. The materials show strong photoluminescence in solution and in the solid state that depends on the electronic nature of the phosphorus center. Electrochemical studies revealed that the phosphorus atom intrinsically furnishes materials with n-channel or ambipolar behavior, also depending on its electronic nature. The experimental data were verified by DFT quantum chemical calculations and suggest that the phosphorus-based heteropentacenes could be excellent candidates for n-channel OFET semiconductor materials.  相似文献   

6.
The structure of 1,3-bis(4,6-dimethyl-1H-nicotinonitrile-1-yl)1,3-dioxy propane polymorphs has been characterized by X-ray diffraction, FT-IR, 1H and 13C NMR spectroscopies. The influence of intra and intermolecular weak interactions is thoroughly studied in solid state using single crystal X-ray diffraction and FT-IR. These polymorphs belong to monoclinic space group 'P2(1/n)' and 'P2(1/c)'. These polymorphs have C-H?n (lone pair), hydrogen bonds, C-N?π, C-H?π and π?π intermolecular non-covalent interactions. These polymorphs are the result of weak interactions and solvent used in crystallization. The FT-IR spectra have been recorded in the solid phase and NMR has been recorded in solvent. The optimized geometry has been calculated by B3LYP methods using different basis sets. The FT-IR and NMR spectra of 1st polymorphs has been calculated at B3LYP/6-31G (d) level. The scaled theoretical wave number showed good agreement with the experimental values. These two polymorphs as well as other stereomers are studied by DFT calculations.  相似文献   

7.
The conformations of three 2',3'-difluoro uridine nucleosides were studied by X-ray crystallography, NMR spectroscopy, and ab initio calculations in an attempt to define the roles that the two vicinal fluorine atoms play in the puckering preferences of the furanose ring. Two of the compounds examined contained fluorine atoms in either the arabino or xylo dispositions at C2' and C3' of a 2',3'-dideoxyuridine system. The third compound also incorporated fluorine atoms in the xylo configuration on the furanose ring but was substituted with a 6-azauracil base in place of uracil. A battery of NMR experiments in D 2O solution was used to identify conformational preferences primarily from coupling constant and NOE data. Both (1)H and (19)F NMR data were used to ascertain the preferred sugar pucker of the furanose ring through the use of the program PSEUROT. Compound-dependent parameters used in the PSEUROT calculations were newly derived from complete sets of conformations calculated from high-level ab initio methods. The solution and theoretical data were compared to the conformations of each molecule in the solid state. It was shown that both gauche and antiperiplanar effects may be operative to maintain a pseudodiaxial arrangement of the C2' and C3' vicinal fluorine atoms. These data, along with previously reported data by us and others concerning monofluorinated nucleoside conformations, were used to propose a model of how fluorine influences different aspects of nucleoside conformations.  相似文献   

8.
Ciprofloxacin is a widely used fluoroquinolone antibiotic. In this work, a comprehensive evaluation of MP2 and DFT with different functionals and basis sets was carried out to select the most suitable level of theory for the study of the NMR properties of ciprofloxacin. Their relative predictive capabilities were evaluated comparing the theoretically predicted and experimental spectral data. Our computational results indicated that in contrast to the solid state, the molecule of ciprofloxacin does not exist as a zwitterion in gaseous state. The results of the calculations of the chemical shifts most close to the experimental were obtained with B3LYP/aug-cc-pVDZ. The F–C coupling constants were calculated systematically with different DFT methods and several basis sets. In general, the calculations of the coupling constants with the BHandH computational method including the applied in this work 6-311++G**, EPRII, and EPRIII basis sets showed a good reproducibility of the experimental values of the coupling constants.  相似文献   

9.
We studied the 1(2)A' '(X2A' '), 1(2)A' (A2A'), 2(2)A' ' (B2A' '), and 2(2)A' (C2A') states of the C2H3Cl+ ion using the complete active space self-consistent field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) methods. For the four ionic states, we calculated the equilibrium geometries, adiabatic (T0) and vertical (Tv) excitation energies, and relative energies (Tv') at the geometry of the molecule at the CASPT2 level and the Cl-loss dissociation potential energy curves (PECs) at the CASPT2//CASSCF level. The computed oscillator strength f value for the X2A' ' <-- A2A' transition is very small, which is in line with the experimental fact that the A state has a long lifetime. The CASPT2 geometry and T0 value for the A2A' state are in good agreement with experiment. The CASPT2 Tv' values for the A2A', B2A' ', and C2A' states are in good agreement with experiment. The Cl-loss PEC calculations predict that the X2A' ', A2A', and C2A' states correlate to C2H3+ (XA1) and the BA' ' state to C2H3+ (1A' ') (the B2A' ' and C2A' PECs cross at R(C-Cl) approximately 2.24 A). Our calculations indicate that at 357 nm the X2A' ' state can undergo a transition to B2A' ' followed by a predissociation of B2A' ' by the repulsive C2A' state (via the B/C crossing), leading to C2H3+ (X1A1), and therefore confirm the experimentally proposed pathway for the photodissociation of X2A' ' at 357 nm. Our CASPT2 D0 calculations support the experimental fact that the X state does not undergo dissociation in the visible spectral region and imply that a direct dissociation of the A state to C2H3+ (X1A1) is energetically feasible.  相似文献   

10.
The isomerization between Z and E isomers of benzaldoximes in different solvents were measured by TLC method. The experimental results show that acid solvents catalyze this inter‐conversion process dramatically. Solution state NMR measurements also show very different spectra for Z and E isomers of benzaldoximes in different solvents. All this suggests that the acidity of solvent is a very important factor to affect the inter‐conversion process. Theoretical investigations of Z to E inter‐conversion of benzaldoximes in different solvents were carried out by DFT calculations at B3LYP/6–3 11+G** level. The calculations show that the barrier from Z to E in the presence of acid is much lower than that without acid. This agrees with the experimental data very well. The calculated structure in the transition state is helpful for the understanding of the inter‐conversion mechanism.  相似文献   

11.
Combined spectroscopic (UV/visible, MS and EPR), electrochemical (CV) and theoretical approaches were used to evaluate the relevant interactions of morin and quercetin, as well as their respective iron(III) complexes with DPPH, tempone, hydroxyl and superoxide radicals. The results on iron complexation specify the stoichiometry and the relevant structural forms entering the chelation of the molecules. The spectroscopic DPPH assay shows better antioxidant activity of quercetin and its iron complex both in terms of EC(50) values and stoichiometry. The results of 2-deoxyribose degradation suggest that antioxidant activities of morin and quercetin may originate from their combined effect of iron chelation and radical scavenging. The distinctive difference in the EPR spectra of morin and quercetin radicals suggests different positions of the radical centers which may account for different sequences of their activities towards investigated radicals. Activity ranking of quercetin and morin, established by cyclic voltammetry, confirms their activity sequence obtained by EPR results and is also in agreement with the results of conformational analysis. The equilibrium geometries, optimized with the M052X functionals and 6-311G(d,p) basis set, predict structural modifications between the ligand molecules in the free state and in the complex structures. The arguments gained through experimental results can also be rationalized in terms of overall molecular geometry and structural features governing antioxidant behavior i.e. substitution pattern of the ring B.  相似文献   

12.
Following earlier reports on the photochemical synthesis of 1,3‐dimethylcyclobutadiene 8 , 10 in a protective host matrix, theoretical calculations for the formation of that adduct have been recently performed by Rzepa. 13 The author formulated criticisms based mainly on density functional theory calculations of 1H NMR spectra. According to Rzepa the calculated spectra do not correspond with our measured spectra, which leads him to the conclusion that our interpretation is wrong, and that mainly cyclobutadiene has not been stabilized or even synthesized; we believe, however, that the initial model that Rzepa used for his calculations does not correspond to chemical reality or is at the very least a crude simplification of it, which implies that his calculations cannot match, in every point, our experimental spectra. Rzepa′s simplified models might be ‘reasonable’ from the theoretical point of view; however, in the case of assessment in the solid state, the theoretical setup does not force the system to preserve the confined stabilizing space defined by the crystalline matrix for encapsulated hosts in the solid state. Inversely, in the case of solution modeling, the theoretical setup is too rigid to properly assess the complex equilibria occurring in solution and to accurately determine the NMR spectra of exchanging species in solution. The inconsistency between our experimental results and the results of the theoretical models proposed by Rzepa is such that his conclusions are considered to be too far from experimental reality. Accurate modeling taking in account “reasonable” experimental details would be a worthwhile endeavor.  相似文献   

13.
Analysis of the microwave spectra of the vibrational ground state of 2-fluorophenyl-isocyanate in the gaseous state shows the existence of a single planar cis conformer. Rotational spectra of the excited torsional states out of the plane and spectra of in-plane vibrations have also been studied. MINDO III type theoretical calculations corroborate the experimental results. Similarly, the configuration of 2-fluorophenylisocyanate in the liquid phase has been studied by NMR using the chemical shift reagent, Eu(fod)3. Induced paramagnetic shifts have been measured on the 13C spectra, for different quantities of the reagent. The results clearly show a higher paramagnetic shift for the carbon bonded to the fluorine atom than for the other nuclei of the aromatic cycle (with the exception of the quaternary carbon), indicating the probable presence of the cis isomer.  相似文献   

14.
Photolysis of dipyrido-[3,2-a:2',3'-c]-phenazine (dppz) (1) in ethanol solution leads to the formation of 9,14-dihydrodipyridophenazine (2), which has been characterised by detailed NMR analysis, UV/VIS absorption spectroscopy, and theoretical calculations which reveal that its red colour is due to a low-lying intramolecular charge transfer state.  相似文献   

15.
Crystal structures and vibrational spectra are reported for the two title molecules which exhibit dual fluorescence due to the existence of a low lying charge transfer excited state. The data show that in the ground state PBN is twisted whereas CPP is planar, and the crystal structures are quite different. The experimental spectra are in very good agreement with quantum mechanical calculations, which also predict considerable differences between the vibrational spectra of CPP in the ground state and in the charge transfer excited state.  相似文献   

16.
The signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump-probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 ? upon illumination. The SAXS/WAXS difference signal for the signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformation, which has an increased radius of gyration, an increased maximum dimension, and a reduced excluded volume. Dynamical annealing calculations using the DEER derived long-range distance restraints in combination with short-range distance information from (1)H-(15)N HSQC perturbation spectroscopy give strong indication for a rearrangement that places part of the N-terminal domain in contact with the exposed chromophore binding cleft while the terminal residues extend away from the core. Time-resolved global structural information from pump-probe TR-SAXS/WAXS data supports this conformation and allows subsequent structural refinement that includes the combined energy terms from DEER, NMR, and SAXS/WAXS together. The resulting ensemble simultaneously satisfies all restraints, and the inclusion of TR-SAXS/WAXS effectively reduces the uncertainty arising from the possible spin-label orientations. The observations are essentially compatible with reduced folding of the I(2)' state (also referred to as the 'pB' state) that is widely reported, but indicates it to be relatively ordered and rearranged. Furthermore, there is direct evidence for the repositioning of the N-terminal region in the I(2)' state, which is structurally modeled by dynamical annealing and refinement calculations.  相似文献   

17.
A quantum chemical study of the Fe[5-NO2-sal-(1,4,7,10)] ((1,10-bis(5-nitrosalicylaldehyde)-1,4,7,10-tetra-ezdecane-O,O',N,N',N' ',N' ')iron(II)) molecule was performed using density functional theory (DFT). Starting from the different X-ray crystallographic structures, geometry optimizations have been performed. These calculations confirmed the conformational isomerism of this complex in each spin states of the molecule ((1)A(1g) and (5)T(2g)). Each employed DFT method (B3LYP, B3LYP*, BP86, HCTH407) reproduced correctly the structural differences between the two calculated conformers when compared to the experimental structures. Furthermore, electronic polarizabilities have been calculated in each spin state and for each conformer. These calculations revealed a higher polarizability in the singlet state in agreement with the measured higher dielectric constant in this state.  相似文献   

18.
A comparative study of 2-(2'-hydroxy-3'-pyridyl)benzimidazole (2',3'-HPyBI), 2-(3'-hydroxy-4'-pyridyl)benzimidazole (3',4'-HPyBI), 2-(4'-hydroxy-3'-pyridyl)benzimidazole (4',3'-HPyBI), 2-(3'-hydroxy-2'-pyridyl)benzimidazole (3',2'-HPyBI), and 2-(5'-hydroxy-4'-pyrimidinyl)benzimidazole (5',4'-HPymBI) with 2-(2'-hydroxyphenyl)benzimidazole (HPBI) was performed theoretically to evaluate the effect of nitrogen substitution in the phenolic ring on the photophysics and rotamerism of HPBI. Density functional theory (DFT) and configuration interaction singles (CIS) combined with time-dependent DFT were employed for ground and excited state studies, respectively. Different possible molecular forms were considered for each molecule viz., cis-enol, trans-enol, open-enol, and keto forms. The computational results revealed that cis-enol is the most stable form in the ground state for all the molecules except in 2',3'-HPyBI. In 2',3'-HPyBI, K-2 keto is the most stable form. Water molecule assisted interconversions between different forms of 2',3'-HPyBI were examined theoretically. Excitation and emission energies for all the forms have been calculated theoretically and the values are in good agreement with the available experimental data. The calculations show that intramolecular proton transfer (ESIPT) is endothermic in the ground state while it is exothermic in the first excited singlet state (except 5',4'-HPymBI). The barrier for the excited state ESIPT reaction increases with nitrogen substitution. Torsional rotation between the benzimidazole and the pyridinyl∕pyrimidinyl rings in the S(1) state depicts that twisted-keto structures involve charge transfer from the hydroxypyridinyl∕hydoxypyrimidinyl to the benzimidazole ring. However, the formation of twisted-keto is not energetically favored in these systems.  相似文献   

19.
We have measured electronic and Raman scattering spectra of 1,1',3,3'-tetraethyl-5,5',6,6'-tetrachloro-benzimidazolocarbocyanine iodide (TTBC) in various environments, and we have calculated the ground state geometric and spectroscopic properties of the TTBC cation in the gas and solution phases (e.g., bond distances, bond angles, charge distributions, and Raman vibrational frequencies) using density functional theory. Our structure calculations have shown that the ground state equilibrium structure of a cis-conformer lies ~200 cm(-1) above that of a trans-conformer and both conformers have C(2) symmetry. Calculated electronic transitions indicate that the difference between the first transitions of the two conformers is about 130 cm(-1). Raman spectral assignments of monomeric- and aggregated-TTBC cations have been aided by density functional calculations at the same level of the theory. Vibrational mode analyses of the calculated Raman spectra reveal that the observed Raman bands above 700 cm(-1) are mainly associated with the in-plane deformation of the benzimidazolo moieties, while bands below 700 cm(-1) are associated with out-of-plane deformations of the benzimidazolo moieties. We have also found that for the nonresonance excited experimental Raman spectrum of aggregated-TTBC cation, the Raman bands in the higher-frequency region are enhanced compared with those in the nonresonance spectrum of the monomeric cation. For the experimental Raman spectrum of the aggregate under resonance excitation, however, we find new Raman features below 600 cm(-1), in addition to a significantly enhanced Raman peak at 671 cm(-1) that are associated with out-of-plane distortions. Also, time-dependent density functional theory calculations suggest that the experimentally observed electronic transition at ~515 nm (i.e., 2.41 eV) in the absorption spectrum of the monomeric-TTBC cation predominantly results from the π → π? transition. Calculations are further interpreted as indicating that the observed shoulder in the absorption spectrum of TTBC in methanol at 494 nm (i.e., 2.51 eV) likely results from the ν(") = 0 → ν' = 1 transition and is not due to another electronic transition of the trans-conformer-despite the fact that measured and calculated NMR results (not provided here) support the prospect that the shoulder might be attributable to the 0-0 band of the cis-conformer.  相似文献   

20.
In this work, the liquid crystal (S)-2-methylbutyl-[4'-(4' '-heptyloxyphenyl)-benzoyl-4-oxy-(S)-2-((S)-2')-benzoyl)-propionyl)]-propionate (ZLL 7/*) was investigated by means of 13C NMR spectroscopy. This compound has a very peculiar mesomorphic behavior, showing the following phases: paraelectric SmA, ferroelectric SmC*, antiferroelectric SmC*A, re-entrant ferroelectric SmC*re, and ferroelectric hexatic Sm*HEX. The structural and orientational ordering properties of ZLL 7/* have been determined by exploiting the nuclear chemical shielding properties of 13C. To this aim, solid-state NMR techniques such as CP, SPINAL-64, and SUPER have been used in combination with DFT calculations. The agreement between experimental and in vacuo DFT shielding parameters appears to be satisfactory. The orientational order parameters obtained from the 13C shielding analysis have been discussed, taking into account different data analysis approaches and comparing them to those previously obtained from an independent 2H NMR study.  相似文献   

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