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1.
2.
Raman scattering and Fourier-transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of two alpha-amino acids (alpha-AAs), i.e., glycine and leucine, were measured in H2O and D2O (at neutral pH and pD). This series of observed vibrational data gave us the opportunity to analyze vibrational features of both AAs in hydrated media by density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing each AA and 12 surrounding water molecules, which represent primary models for hydration scheme of amino acids, allowed us to assign the main observed peaks.  相似文献   

3.
The biological relevance of amino acids is well known. They can be used as zwitterionic, cationic or anionic forms according to the pH of the medium where they are. Thus, our aim herein was to study the conformational preference of the polar amino acid l-threonine [C4H9NO3, (2S,3R)-2-amino-3-hydroxybutyric acid] under different pH conditions. A conformational study in an aqueous solution of the dissociation equilibrium of the amino acid l-threonine was carried out for this purpose. We recorded, at room temperature, the Mid-IR, Far-IR, Raman and VCD spectra of l-threonine from the aqueous solutions at pH values 5.70 (zwitterionic species), 1.00 (protonated species) and 13.00 (deprotonated species). The number of conformers found with the conformational search was 9 zwitterions, 27 anions and 52 cations. Both the study of the conformational landscape and the theoretical analysis of the vibrational features were accomplished by using DFT and ab initio calculations, that is, B3LYP/6-311++G(d,p) level of theory for all the conformers obtained from the conformational search, M062X/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory for the most stable conformers. The presence of water was included with the IEF-PCM implicit hydration model. With regard to the zwitterion, the importance of the analysis of the low frequency region (700–30 cm–1) in the Far-IR spectra should be noted, because it provides relevant information that can be used to determine the presence of the most stable structures.  相似文献   

4.
The conformational distributions of N‐acetyl‐L ‐cysteine (NALC) in aqueous solutions at several representative pH values are investigated using vibrational absorption (VA), UV/Vis, and vibrational circular dichroism (VCD) spectroscopy, together with DFT and molecular dynamics (MD) simulations. The experimental VA and UV/Vis spectra of NALC in water are obtained under strongly acid, neutral, and strongly basic conditions, as well as the VCD spectrum at pH 7 in D2O. Extensive searches are carried out to locate the most stable conformers of the protonated, neutral, deprotonated, and doubly deprotonated NALC species at the B3LYP/6‐311++G(d,p) level. The inclusion of the polarizable continuum model (PCM) modifies the geometries and the relative stabilities of the conformers noticeably. The simulated PCM VA spectra show significantly better agreement with the experimental data than the gas‐phase ones, thus allowing assignment of the conformational distributions and dominant species under each experimental condition. To further properly account for the discrepancies noted between the experimental and simulated VCD spectra, PCM and the explicit solvent model are utilized. MD simulations are used to aid the modelling of the NALC–(water)N clusters. The geometry optimization, harmonic frequency calculations, and VA and VCD intensities are computed for the NALC–(water)3,4 clusters at the B3LYP/6‐311++G(d,p) level without and with the PCM. The inclusion of both explicit and implicit solvation models at the same time provides a decisively better agreement between theory and experiment and therefore conclusive information about the conformational distributions of NALC in water and hydrogen‐bonding interactions between NALC and water molecules.  相似文献   

5.
The nitrogen K-edge spectra of aqueous proline and diglycine solutions have been measured by total electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at neutral and high pH. All observed spectral features have been assigned by comparison to the recently reported spectrum of aqueous glycine and calculated spectra of isolated amino acids and hydrated amino acid clusters. The sharp preedge resonances at 401.3 and 402.6 eV observed in the spectrum of anionic glycine indicate that the nitrogen terminus is in an "acceptor-only" configuration, wherein neither amine proton is involved in hydrogen bonding to the solvent, at high pH. The analogous 1s --> sigma(NH) preedge transitions are absent in the NEXAFS spectrum of anionic proline, implying that the acceptor-only conformation observed in anionic glycine arises from steric shielding induced by free rotation of the amine terminus about the glycine CN bond. Anionic diglycine solutions exhibit a broadened 1s --> pi(CN) resonance at 401.2 eV and a broad shoulder resonance at 403 eV, also suggesting the presence of an acceptor-only species. Although this assignment is not as unambiguous as for glycine, it implies that the nitrogen terminus of most proteins is capable of existing in an acceptor-only conformation at high pH. The NEXAFS spectrum of zwitterionic lysine solution was also measured, exhibiting features similar to those of both anionic and zwitterionic glycine, and leading us to conclude that the alpha amine group is present in an acceptor-only configuration, while the end of the butylammonium side chain is fully solvated.  相似文献   

6.
A full structural search of the canonical, zwitterionic, protonated and deprotonated lysine conformers in gas phase is presented. A total of 17,496 canonical, 972 zwitterionic, 11,664 protonated and 1458 trial deprotonated structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were initially optimized at the AM1 level, and the resulting structures were determined at the B3LYP/6-311G* level. A total of 927 canonical, 730 protonated and 193 deprotonated conformers were found, but there were no stable zwitterionic structures in the gas phase. The most stable conformers of the canonical, protonated and deprotonated lysine were further optimized at the B3LYP/6-311++G** level. The energies of the most stable structures were determined at the MP2/6-311G(2df,p) level and the vibrational frequencies were calculated at the B3LYP/6-311++G** level. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, vertical ionization energies, enthalpies, Gibbs free energies and conformational distributions of gaseous lysine were presented. Numerous new structures are found and the lowest-energy lysine conformer is more stable than the existing one by 1.1 kcal/mol. Hydrogen bonds are classified and may cause significant red-shifts to the associated vibrational frequencies. The calculated proton affinity/dissociation energy and gas-phase basicity/acidity are in good agreement with the experiments. Calculations are also presented for the canonical lysine–H2O and zwitterionic lysine–H2O clusters. Interaction between lysine and H2O significantly affects the relative conformational stabilities. Only one water molecule is sufficient to produce the stable zwitterionic structures in gas phase. The lowest-energy structure is found to be zwitterions when applying the conductor-like polarized continuum solvent model (CPCM) to the lysine–H2O complexes.  相似文献   

7.
Gas phase vibrational spectra of dimethyl methylphosphonate (DMMP), trimethyl phosphate (TMP), and triethyl phosphate (TEP) have been measured using FTIR spectroscopy. For DMMP, TMP, and TEP, most of the infrared active vibrational modes have been observed in the 50-5000 cm (-1) spectral range, allowing an unambiguous discrimination between the three molecules. The vibrational analysis of the spectra was performed by comparing with MP2 and B3LYP harmonic and anharmonic force field ab initio calculations. The extension to anharmonic calculations provides the best agreement for the mid-infrared and the near-infrared spectra, but they do not improve the harmonic frequency predictions in the far-infrared domain. This part of the vibrational spectra associated with collective and nonlocalized vibrational modes presents the largest frequency differences between the two lowest energy conformers of DMMP and TMP. These two conformers were taken into account in the vibrational assignment of the spectra. Their experimental evidence was obtained by deconvoluting vibrational bands in the mid-infrared and in the far-infrared regions, respectively. For TEP, the conformational landscape appears very complicated at ambient temperature, and a further analysis at low temperature is required to explain the vibrational features of each conformer.  相似文献   

8.
Structure, stability, and vibrational IR and Raman spectra of I(2)(*-) x nCO(2) clusters (n = 1-10) are reported based on first-principle electronic structure calculations. Several close-lying minimum energy structures are predicted for these solvated clusters following the quasi Newton-Raphson procedure of geometry optimization. Search strategy based on Monte-Carlo simulated annealing is also applied to find out the global minimum energy structures of these clusters. Successive addition of solvent CO(2) molecules to the negatively charged diatomic solute, I(2)(*-), is fairly symmetrical. Energy parameters of these solvated clusters are calculated following second-order Moller-Plesset perturbation (MP2) as well as coupled cluster theory with 6-311+G(d) set of basis function (I atom is treated with 6-311G(d) set of basis function). The excess electron in these solvated clusters is observed to be localized mainly over the two I atoms. Average interaction energy between the anionic solute, I(2)(*-), and a solvent CO(2) molecule is approximately 129 meV in I(2)(*-) x nCO(2) clusters, and the average interaction energy between two solvent CO(2) molecules is approximately 85 meV in the case of neutral (CO(2))(n) clusters at MP2 level of theory. IR spectra show similar features in all these solvated clusters, depicting a strong band at approximately 2330 cm(-1) for C-O stretching and a weak band at approximately 650 cm(-1) for CO(2) bending modes. Degeneracy of the bending mode of a free solvent CO(2) unit gets lifted when it interacts with the charged solute I(2)(*-) to form a molecular cluster because of the change in structure of solvent CO(2) units. The vibrational band at the bending region of CO(2) in the Raman spectra of these anionic clusters shows a characteristic feature for the formation of I(2)(*-) x nCO(2) clusters showing a Raman band at approximately 650 cm(-1).  相似文献   

9.
Glutathione tripeptide (γ-glutamyl-cysteinyl-glycine) is a flexible molecule and its conformational energy landscape is strongly influenced by forming intramolecular hydrogen bond, its charge and the environment. This study employs DFT-B3LYP method with the 6-31+G (d,p) basis set to carry out conformational analysis of neutral, zwitterionic, cationic, and anionic forms of glutathione. In analyzing the structural characteristics of these structures, intramolecular hydrogen bonds were identified and characterized in details by topological parameters such as electron density ρ(r) and Laplacian of electron density $ \nabla^{2} $ ρ(r) from Bader’s atom in molecules theory. Charge transfer energies based on natural bond orbital analysis are also considered to interpret these intramolecular hydrogen bonds. Our results show that these hydrogen bonds are partially electrostatic and partially covalent in nature, in which the covalent contribution increases as the stabilization energy of hydrogen bond increases. Furthermore, the back bone and side chain (Ramachandran map) orientations of various ionic forms of glutathione have been studied and conformation of each constitution of glutathione tripeptide (i.e., Glu, Cys, and Gly moieties) was determined. In most species side chain conformation were found to be hindered gauche–gauche orientation by intramolecular hydrogen bonds.  相似文献   

10.
The first gas-phase vibrational spectra are presented for several anionic iron carbonyl clusters, ranging in size from Fe(CO)4- to Fe5(CO)14- in the CO-stretching region (1600-2100 cm-1). The experimental spectra provide some immediate structural information about the clusters in the form of low-wavenumber (1750-1850 cm-1) bands marking the presence of bridging carbonyl ligands (mu2-COs). Supporting DFT calculations are presented for the smaller clusters (<3 Fe atoms) and give good agreement with the experimental data, allowing structural assignments for these cases. The Fe2(CO)7- spectrum suggests a structure lacking bridging carbonyl ligands, in agreement with the DFT results. For the case of Fe2(CO)8-, there are two possible structures based on the calculations, both with and without bridging carbonyls. The presence of a low-frequency band ( approximately 1770 cm-1) in the experimental spectrum conclusively demonstrates the existence of the bridged form. The ramifications of these data for metal-metal bonding in the clusters are also considered.  相似文献   

11.
The structures of neutral boron clusters, B(11), B(16), and B(17), have been investigated using vibrational spectroscopy and ab initio calculations. Infrared absorption spectra in the wavelength range of 650 to 1550 cm(-1) are obtained for the three neutral boron clusters from the enhancement of their near-threshold ionization efficiency at a fixed UV wavelength of 157 nm (7.87 eV) after resonant absorption of the tunable infrared photons. All three clusters, B(11), B(16), and B(17), are found to possess planar or quasi-planar structures, similar to their corresponding anionic counterparts (B(n) (-)), whose global minima were found previously to be planar, using photoelectron spectroscopy and theoretical calculations. Only minor structural changes are observed between the neutral and the anionic species for these three boron clusters.  相似文献   

12.
It has been discussed in the literature that electron delocalization along the peptide backbone and side chain modulates the physical and chemical features of peptides and proteins. The structure and properties of peptides are determined by their charge‐density distribution, such that the modification of its side chain plays an important role on its electronic structure and physicochemical properties. Research on Entamoeba histolytica soluble factors led to the identification of the pentapeptide Met‐Gln‐Cys‐Asn‐Ser, with anti‐inflammatory in vivo and in vitro effects. A synthetic pentapeptide, Met‐Pro‐Cys‐Asn‐Ser, maintained the same anti‐inflammatory actions in experimental assays. A previous theoretical study allowed proposing the Cys‐Asn‐Ser tripeptide (CNS tripeptide) as the pharmacophore group of both molecules. This theoretical hypothesis was recently confirmed experimentally. The objective of this work was to study the influence of the electron donor and electron withdrawing substituent groups on the electronic structure and physicochemical properties of the CNS tripeptide derivatives through a theoretical study at the density functional theory level of theory. Our results in deprotonation energies showed that the relative acidity of hydrogen atom (H2) of the serine‐amide group increases with the electron withdrawing groups. This result was confirmed by means of a study of bond order. The proton affinities illustrated that the electron donor groups favored the basicity of the amino group of the cysteine amino acid. Atomic charges, Frontier molecular orbitals (HOMO–LUMO), and electrostatic potential isosurface and its geometric parameters permitted to analyze the effect that provoked the electron donor and electron attractor groups on its electronic structure and physicochemical features and to identify some reactive sites that could be associated with the anti‐inflammatory activity of tripeptide CNS derivatives. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2398–2410, 2010  相似文献   

13.
One water molecule stabilizes the cationized arginine zwitterion   总被引:1,自引:0,他引:1  
Singly hydrated clusters of lithiated arginine, sodiated arginine, and lithiated arginine methyl ester are investigated using infrared action spectroscopy and computational chemistry. Whereas unsolvated lithiated arginine is nonzwitterionic, these results provide compelling evidence that attachment of a single water molecule to this ion makes the zwitterionic form of arginine, in which the side chain is protonated, more stable. The experimental spectra of lithiated and sodiated arginine with one water molecule are very similar and contain spectral signatures for protonated side chains, whereas those of lithiated arginine and singly hydrated lithiated arginine methyl ester are different and contain spectral signatures for neutral side chains. Calculations at the B3LYP/6-31++G** level of theory indicate that solvating lithiated arginine with a single water molecule preferentially stabilizes the zwitterionic forms of this ion by 25-32 kJ/mol and two essentially isoenergetic zwitterionic structure are most stable. In these structures, the metal ion either coordinates with the N-terminal amino group and an oxygen atom of the carboxylate group (NO coordinated) or with both oxygen atoms of the carboxylate group (OO coordinated). In contrast, the OO-coordinated zwitterionic structure of sodiated arginine, both with and without a water molecule, is clearly lowest in energy for both ions. Hydration of the metal ion in these clusters weakens the interactions between the metal ion and the amino acid, whereas hydrogen-bond strengths are largely unaffected. Thus, hydration preferentially stabilizes the zwitterionic structures, all of which contain strong hydrogen bonds. Metal ion size strongly affects the relative propensity for these ions to form NO or OO coordinated structures and results in different zwitterionic structures for lithiated and sodiated arginine clusters containing one water molecule.  相似文献   

14.
The neurotransmitter analogue p-aminophenethylamine (APEA) illustrates many of the pitfalls and challenges associated with spectroscopic and conformational analysis of flexible molecules. The combined experimental-theoretical study presented here resolves a long-standing controversy over its conformational energetic preferences. Jet-cooled resonance enhanced two-photon ionisation (R2PI) and IR-UV ion depletion techniques enabled conformer-specific IR spectra in the NH-CH stretch region to be measured for four distinct conformers of APEA. Comparison of spectra with theoretical calculations (including MP2, M06-2X and B3LYP with aug-cc-pVTZ basis sets) allows the two most populated conformers to be unambiguously identified as those having a gauche arrangement of the side chain, which facilitates an NH···π type hydrogen bond. The other two observed conformers are assigned to structures with an anti-side chain. A fifth gauche conformer, predicted to be least stable, is not observed. Comparison with published conformer specific IR spectra of tyramine (Makara et al., J. Phys. Chem. A, 2008, 112, 13463-13469) and Raman spectra of phenylethylamine (Golan et al., J. Chem. Phys., 2009, 131, 024305) reveals an entirely consistent pattern of spectral signatures associated with the four specific conformations of the ethylamine side chain evident in APEA, and aids assignment of the associated CH and NH stretch fundamentals, some of which have very weak IR intensities. Extensive calculations of the relative energetic trends of the five conformers have been carried out. In comparison to the highest level of theory considered, CCSD(T)-F12b/cc-pVDZ-F12, MP2 overestimate the energy difference, whereas DFT significantly underestimates the energetic preference for NH···π stabilised gauche conformers, although inclusion of dispersion (M06-2X, B3LYP-D3) improves the DFT results.  相似文献   

15.
The molecular structures of low-lying isomers of anionic and neutral sodium auride clusters have been studied computationally at the second-order M?ller-Plesset perturbation theory level using quadruple-ζ basis sets augmented with a double set of polarization functions. The first vertical detachment energies were calculated at the M?ller-Plesset level as the energy difference between the cluster anion and the corresponding neutral cluster. The photodetachment energies of higher-lying ionization channels were calculated by adding electronic excitation energies of the neutral clusters to the first vertical detachment energy. The excitation energies were calculated at the linear response approximate coupled-cluster singles and doubles level using the anionic cluster structures. The obtained ionization energies for NaAu(-), NaAu(2)(-), NaAu(3)(-), NaAu(4)(-), Na(2)Au(2)(-), Na(2)Au(3)(-), Na(3)Au(3)(-), and Na(2)Au(4)(-) were compared to values deduced from experimental photoelectron spectra. Comparison of the calculated photoelectron spectra for a few energetically low-lying isomers shows that the energetically lowest cluster structures obtained in the calculations do not always correspond to the clusters produced experimentally. Spin-component-scaled second-order M?ller-Plesset perturbation theory calculations shift the order of the isomers such that the observed clusters more often correspond to the energetically lowest structure, whereas the spin-component-scaled approach does not improve the photodetachment energies of the sodium aurides. The potential energy surface of the sodium aurides is very soft, with several low-lying isomers requiring an accurate electron correlation treatment. The calculations show that merely the energetic criterion is not a reliable means to identify the structures of the observed sodium auride clusters; other experimental information is needed to ensure a correct assignment of the cluster structures. The cluster structures of nonstoichiometric anionic sodium aurides have been determined by comparing calculated ionization energies for low-lying structures of the anionic clusters with experimental data.  相似文献   

16.
The mixed micelle formation in aqueous solutions between an anionic gemini surfactant derived from the amino acid cystine (C(8)Cys)(2), and the phospholipids 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC, a micelle-forming phospholipid) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC, a vesicle-forming phospholipid) has been studied by conductivity and the results compared with the ones obtained for the mixed systems with the single-chain surfactant derived from cysteine, C(8)Cys. Phospholipid-surfactant interactions were found to be synergistic in nature and dependent on the type of phospholipid and on surfactant hydrophobicity. Regular solution theory was used to analyse the gemini surfactant-DHPC binary mixtures and the interaction parameter, β(12), has been evaluated, as well as mixed micelle composition. The results have been interpreted in terms of the interplay between reduction of the electrostatic repulsions among the ionic head groups of the surfactants and steric hindrances arising from incorporation of the zwitterionic phospholipids in the mixed micelles.  相似文献   

17.
Vibrational circular dichroism (VCD) spectroscopy is utilized to reveal the detailed conformational distributions of the dominant serine species in aqueous solutions under three representative pH conditions of 1.0, 5.7, and 13.0, together with vibrational absorption (VA) spectroscopy, density functional theory (DFT), and molecular dynamics simulation. The experimental VA and VCD spectra of serine in H2O and D2O in the fingerprint region under three pH values are obtained. DFT calculations at the B3LYP/6‐311++G(d,p) level are carried out for the protonated, zwitterionic, and deprotonated serine species. The lowest‐energy conformers of all three species are identified and their corresponding VA and VCD spectra simulated. A comparison between the gas‐phase simulations and the experimental VA and VCD spectra suggests that one or two of the most stable conformers of each species contribute predominantly to the observed data, although some discrepancies are noted. To account for the solvent effects, both the polarizable continuum model and the explicit solvation model are considered. Hydrogen‐bonded protonated, zwitterionic, and deprotonated serine–(water)6 clusters are constructed based on radial distribution function analyses and molecular dynamics snapshots. Geometry optimization and VA and VCD simulations are performed for these clusters at the B3LYP/6‐311++G(d,p) level. Inclusion of the explicit water molecules is found to improve the agreement between theory and experiment noticeably in all three cases, thus enabling conclusive conformational distribution analyses of serine in aqueous solutions directly.  相似文献   

18.
This paper reports the pH-induced structural changes in the surface immobilized poly(L-lysine)(PLL)film.Two-dimensional(2D) correlation analysis was applied to the Fourier transform infrared(FTIR)spectra of the surface-immobilized PLL film to examine the spectral changes induced by the alternations of the protonation state of the amino group in the side chain.Significant spectral changes in the FTIR spectra of the PLL film were observed between pH 7 and 8.The decrease in the protonation state of the amino group in the side chain induced spectral changes in the amino group as well as conformational changes in the alky]group in the side chain.From pH 1-8,the spectral changes in the amino and alkyl groups in the side chain occurred before those of the amide group in the main chain of the surface immobilized PLL film.  相似文献   

19.
The UV–vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV–vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua‐p‐Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV–vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical–computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc.  相似文献   

20.
IR and spectra of the L-ascorbic acid (L-AA) also known as vitamin C have been recorded in the region 4000-50 cm(-1). In order to make vibrational assignments of the observed IR and Raman bands computations were carried out by employing the RHF and DFT methods to calculate the molecular geometries and harmonic vibrational frequencies along with other related parameters for the neutral L-AA and its singly charged anionic (L-AA(-)) and cationic (L-AA(+)) species. Significant changes have been found for different characteristics of a number of vibrational modes. The four ν(O-H) modes of the L-AA molecule are found in the order ν(O(9)-H(10))>ν(O(19)-H(20))>ν(O(7)-H(8))>ν(O(14)-H(15)) which could be due to complexity of hydrogen bonding in the lactone ring and the side chain. The CO stretching wavenumber (ν(46)) decreases by 151 cm(-1) in going from the neutral to the anionic species whereas it increases by 151 cm(-1) in going from the anionic to the cationic species. The anionic radicals have less kinetic stabilities and high chemical reactivity as compared to the neutral molecule. It is found that the cationic radical of L-AA is kinetically least stable and chemically most reactive as compared to its neutral and anionic species.  相似文献   

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