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1.
Small ; 20(35): e2401264, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38634249

ABSTRACT

Biological photo-responsive ion channels play important roles in the important metabolic processes of living beings. To mimic the unique functions of biological prototypes, the transition metal dichalcogenides, owing to their excellent mechanical, electrical, and optical properties, are already used for artificial intelligent channel constructions. However, there remain challenges to building artificial bio-semiconductor nanochannels with finely tuned band gaps for accurately simulating or regulating ion transport. Here, two well-designed peptides are employed for the WS2 nanosheets functionalization with the sequences of PFPFPFPFC and DFDFDFDFC (PFC and DFC; P: proline, D: aspartate, and F: phenylalanine) through cysteine (Cys, C) linker, and an asymmetric peptide-WS2 membrane (AP-WS2M) could be obtained via self-assembly of peptide-WS2 nanosheets. The AP-WS2M could realize the photo-driven anti-gradient ion transport and vis-light enhanced osmotic energy conversion by well-designed working patterns. The photo-driven ion transport mechanism stems from a built-in photovoltaic motive force with the help of formed type II band alignment between the PFC-WS2 and DFC-WS2. As a result, the ions would be driven across the channels of the membrane for different applications. The proposed system provides an effective solution for building photo-driven biomimetic 2D bio-semiconductor ion channels, which could be extensively applied in the fields of drug delivery, desalination, and energy conversion.


Subject(s)
Ion Channels , Ion Transport , Peptides , Peptides/chemistry , Ion Channels/metabolism , Ion Channels/chemistry , Light
2.
Nucleic Acids Res ; 50(D1): D150-D160, 2022 01 07.
Article in English | MEDLINE | ID: mdl-34718746

ABSTRACT

Noncanonical nucleic acid structures, such as G-quadruplex (G4) and i-Motif (iM), have attracted increasing research interests because of their unique structural and binding properties, as well as their important biological activities. To date, thousands of small molecules that bind to varying G4/iM structures have been designed, synthesized and tested for diverse chemical and biological uses. Because of the huge potential and increasing research interests on G4-targeting ligands, we launched the first G4 ligand database G4LDB in 2013. Here, we report a new version, termed G4LDB 2.2 (http://www.g4ldb.com), with upgrades in both content and function. Currently, G4LDB2.2 contains >3200 G4/iM ligands, ∼28 500 activity entries and 79 G4-ligand docking models. In addition to G4 ligand library, we have also added a brand new iM ligand library to G4LDB 2.2, providing a comprehensive view of quadruplex nucleic acids. To further enhance user experience, we have also redesigned the user interface and optimized the database structure and retrieval mechanism. With these improvements, we anticipate that G4LDB 2.2 will serve as a comprehensive resource and useful research toolkit for researchers across wide scientific communities and accelerate discovering and validating better binders and drug candidates.


Subject(s)
Databases, Genetic , G-Quadruplexes , Structure-Activity Relationship , Binding Sites/genetics , Humans , Ligands , Molecular Docking Simulation
3.
Inorg Chem ; 61(46): 18789-18794, 2022 Nov 21.
Article in English | MEDLINE | ID: mdl-36350982

ABSTRACT

Developing smart stimuli-responsive metal-organic frameworks (MOFs) with diversified induced readable signals is highly desirable; however, reported multimode responsive MOFs are always achieved under strong environmental stimulations, making it difficult to keep MOF structures stable for practical applications. Herein, we reported a hydration-facilitated coordination tuning strategy to achieve the dual-mode water response in fluorescence and proton conduction from a single MOF. The designed MOF permitted reversible single-crystal transformation via the controllable hydration effect on metal nodes. The change in coordination modes leads to the regulation on conformations of optical ligands, contributing to the switch of fluorescence emissions. Moreover, the hydration effect adds additional hydrogen-bond sites in channels and optimizes hydrogen-bond networks, abruptly enhancing the proton conductivity by ∼20 times. These results pave new avenues for the exploitation of smart MOFs with multimode responsive behavior for on-demand sensing/detection applications.

4.
Angew Chem Int Ed Engl ; 61(51): e202213959, 2022 12 19.
Article in English | MEDLINE | ID: mdl-36259375

ABSTRACT

Rational design of hydrogen-bonded organic frameworks (HOFs) with multiple functionalities is highly sought after but challenging. Herein, we report a multifunctional HOF (HOF-FJU-2) built from 4,4',4'',4'''-(9H-carbazole-1,3,6,8-tetrayl)tetrabenzaldehyde molecule with tetrabenzaldeyde for their H bonding interactions and carbazole N-H site for its specific recognition of small molecules. The Lewis acid N-H sites allow HOF-FJU-2 facilely separate acetone from its mixture with another solvent like methanol with smaller pKa value. The donor (D)-π-acceptor (A) aromatic nature of the organic building molecule endows this HOF with solvent dependent luminescent/chromic properties, so the column acetone/methanol separation on HOF-FJU-2 can be readily visualized.


Subject(s)
Acetone , Methanol , Binding Sites , Solvents , Hydrogen
5.
Phys Chem Chem Phys ; 21(41): 23026-23035, 2019 Oct 24.
Article in English | MEDLINE | ID: mdl-31599895

ABSTRACT

The knowledge of intramolecular vibrational energy redistribution (IVR) and structural dynamics of rhenium photo-catalysts is essential for understanding the mechanism of the photo-catalytic process of CO2 reduction. In this study, the rhenium compound Re(dcbyp)(CO)3NCS (Re-NCS), which served as a model CO2 reduction catalyst, was investigated using two dimensional infrared (2D IR) spectroscopy. The vibrational relaxation dynamics and rotational dynamics of Re-NCS were measured by monitoring both the CO and NCS vibrational modes. The rotational dynamics measurement of the CO vibrational stretch shows a single exponential decay with a time constant of 140 ± 10 ps. In contrast, a bi-exponential decay is needed to describe the rotational dynamics of the NCS stretching mode with time constants of 1.5 ± 0.3 ps and 189 ± 15 ps. The 2D IR experiment indicated that the carbonyl CO vibrational modes in Re-NCS are strongly coupled. Furthermore, the intramolecular vibrational energy transfer between CO and NCS stretching modes was observed and analyzed based on an energy exchange model. The energy down flowing transfer from CN to CO stretching mode was determined using time constants of 50 ps. The relatively slow intramolecular vibrational energy transfer rate suggests that there is a weak coupling between CO and NCS ligands. Further theoretical calculation showed that the coupling strength between CO and CN is relatively weak and is about 5-6 times smaller than the coupling strength between the CO vibrational modes in Re-NCS. The distinct structural dynamics of the NCS ligand in Re-NCS presented in this study should provide a fundamental understanding of the role of an anionic ligand in rhenium photo-catalysts, which is believed to play an important role in the photo-catalytic reduction of CO2.

6.
Water Res ; 256: 121611, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38640567

ABSTRACT

Natural small molecular organic matter (NSOM), ubiquitous in natural waters and distinct from humic acid or fulvic acid, is a special type of dissolved organic matter (DOM) which is characterized as strong photosensitivity and simple molecular structure. However, little study had been directed on the role of NSOM in eliminating emerging contaminants in advanced reduction process (ARP). This study took three small molecular isomeric organic acids (p-hydroxybenzoic acid, pHBA; salicylic acid, SA; m-hydroxybenzoic acid, mHBA) as the representative substances of NSOM to explore these mechanisms on promoting Ribavirin (RBV, an anti COVID-19 medicine) degradation in ultraviolet activated sulfite (UV/Sulfite) process. The results demonstrated that the observed degradation rate constant of RBV (kobs-RBV) was 7.56 × 10-6 s-1 in UV/Sulfite process, indicating that hydrated electron (eaq-) from UV/Sulfite process could not effectively degrade RBV, while it increased by 178 and 38 times when pHBA and SA were introduced into UV/Sulfite process respectively, suggesting that pHBA and SA strongly promoted RBV degradation while mHBA had no promotion on RBV abatement in UV/Sulfite process. Transient absorption spectra and reactive intermediates scavenging experiment indicated that the triplet excited state pHBA and SA (3pHBA* and 3SA*) contributed to the degradation of RBV through non-radical process. Notably, eaq- played the role of key initiator in transforming pHBA and SA into their triplet states. The difference of kobs-RBV in UV/Sulfite/pHBA and UV/Sulfite/SA process was attributed to different generation pathways of 3pHBA* and 3SA* (high molar absorptivity at the wavelength of 254 nm and photosensitive cycle, respectively) and their second order rate constants towards RBV (kRBV-3pHBA* = 8.60 × 108 M-1 s-1 and kRBV-3SA* = 6.81 × 107 M-1 s-1). mHBA could not degrade RBV for its lack of intramolecular hydrogen bond and low molar absorptivity at 254 nm to abundantly transform into its triplet state. kobs-RBV increased as pH increased from 5.0 to 11.0 in UV/Sulfite/SA process, due to the high yield of eaq- in alkaline condition which promoted the generation of 3SA* and the stable of the absorbance of SA at 254 nm. By contrast, kobs-RBV underwent a process of first increasing and then decreasing in UV/Sulfite/pHBA process as the increase of pH, and its highest value achieved in a neutral condition. This lied in the exposure of eaq- increased as the increase of pH which promoted the generation of 3pHBA*, while the molar absorptivity of pHBA at 254 nm decreased as the increase of pH in an alkaline condition which inhibited the yield of 3pHBA*. The RBV degradation pathways and products toxicity assessment indicated that UV/Sulfite/pHBA had better detoxification performance on RBV than UV/Sulfite/SA process. This study disclosed a novel mechanism of emerging contaminants abatement through non-radical process in NSOM mediated ARP, and provide a wide insight into positive profile of DOM in water treatment process, instead of only taking DOM as a quencher of reactive intermediates.


Subject(s)
Antiviral Agents , Antiviral Agents/chemistry , Ultraviolet Rays , Sulfites/chemistry
7.
Environ Sci Pollut Res Int ; 31(35): 48164-48174, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39017866

ABSTRACT

Ribavirin (RBV), which is extensively used to treat viral diseases such as COVID-19, is considered one of the major emerging contaminants due to its long-term existence and health risk in the aqueous environmental system. However, research on effective removal of RBV still remains insufficient. In this study, we investigated the RBV degradation kinetics and mechanism in UV/chlorine/Fe(II) process. The degradation rate constant kobs-RBV of RBV was 2.52 × 10-4 s-1 in UV/chlorine/Fe(II) process, which increased by 1.6 times and 1.3 times than that in chlorine alone and UV/chlorine process, respectively. Notably, trace amount Fe(II) promoted RBV degradation in UV/chlorine system through Fe2+/Fe3+ cycles, enhancing the yield of reactive species such as HO· and certain species reactive chlorine radicals (RCS). The contributions of HO· and RCS toward RBV degradation were 53.91% and 16.11%, respectively. Specifically, Cl·, ClO·, and Cl2·- were responsible for 8.59%, 2.69%, and 4.83% of RBV removal. The RBV degradation pathway indicated that the reactive species preferentially attacked the amide moiety of RBV, which cleaved the ether bond and the hydroxyl group. The toxicity evaluation of RBV degradation products elucidated that UV/chlorine/Fe(II) process was beneficial for RBV detoxification.


Subject(s)
Chlorine , Iron , Ribavirin , Ultraviolet Rays , Water Pollutants, Chemical , Water Purification , Water Purification/methods , Chlorine/chemistry , Water Pollutants, Chemical/chemistry , Ribavirin/chemistry , Iron/chemistry , Kinetics
8.
Spectrochim Acta A Mol Biomol Spectrosc ; 292: 122424, 2023 May 05.
Article in English | MEDLINE | ID: mdl-36750008

ABSTRACT

The amide-I vibrational characteristics and conformational preferences of the model compound - histidine dipeptide (Ac-His-NHCH3, HISD) in gas phase and solution have been revealed with the help of ab initio calculations and wavefunction analyses. The Gibbs free energy surfaces (FESs) of solvated HISD were smoothed by solvent effect to exhibit different structural populations concerning various external environments. It was shown that the most stable conformations of HISD in CHCl3 and gas phase are C7eq, while those in DMSO and water are ß and PPII, respectively. Compared with ALAD, the number of accessible conformational states on these FESs was predicted to be reduced due to the steric effect of imidazole group. The two amide-I normal modes of HISD were found to have intrinsically secondary structural dependencies, and be sensitive to surrounding environments. The average amide-Ia frequencies of HISD isomers in these environments were predicted to be almost the same as those of ALAD, while the amide-Ib mean frequencies were estimated to be lower than ALAD due to the intramolecular interactions between the imidazole group and amino-terminal amide unit. The good linear correlations between amide-I frequencies and the atomic electrostatic potentials (ESPs) of amide groups were also found to interpret the solvent-induced amide-I frequency shifts of HISD at the electronic structure level. These results allow us to gain a deep understanding of amide-I vibrations of HISD, and would be helpful for the site-specific conformational monitoring and spectral interpretation of solvated polypeptides.


Subject(s)
Amides , Dipeptides , Amides/chemistry , Dipeptides/chemistry , Histidine , Vibration , Solvents/chemistry
9.
Spectrochim Acta A Mol Biomol Spectrosc ; 268: 120675, 2022 Mar 05.
Article in English | MEDLINE | ID: mdl-34890871

ABSTRACT

Infrared spectroscopy is a powerful tool for the understanding of molecular structure and function of polypeptides. Theoretical interpretation of IR spectra relies on ab initio calculations may be very costly in computational resources. Herein, we developed a neural network (NN) modeling protocol to evaluate a model dipeptide's backbone amide-I spectra. DFT calculations were performed for the amide-I vibrational motions and structural parameters of alanine dipeptide (ALAD) conformers in different micro-environments ranging from polar to non-polar ones. The obtained backbone dihedrals, C = O bond lengths and amide-I frequencies of ALAD were gather together for NN architecture. The applications of built NN protocols for the prediction of amide-I frequencies of ALAD in other solvation conditions are quite satisfactory with much less computational cost comparing with electronic structure calculations. The results show that this cost-effective way enables us to decipher the polypeptide's dynamic secondary structures and biological functions with their backbone vibrational probes.


Subject(s)
Amides , Dipeptides , Alanine , Molecular Dynamics Simulation , Neural Networks, Computer , Spectrophotometry, Infrared , Vibration
10.
J Environ Chem Eng ; 10(6): 108641, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36186959

ABSTRACT

Chloroquine Phosphate (CP) is an antiviral drug used for treatment of COVID-19. It is released into wastewater and eventually contaminates natural water. This study reports an effective homogeneous catalysis way for CP degradation by the 2,2,6,6-Tetramethylpiperidine-N-oxyl (TEMPO) enhanced persulfate (PDS) activation under UVB-LEDs irradiation at 305 nm. TEMPO at a low concentration (0.1 µM) enhanced CP degradation in UV305/PDS process in deionized water at different pHs, in different anions and different molecular weight dissolved organic matter solutions and in real surface water. The enhancement was verified to be attributed to the electron shuttle role of TEMPO, which promoted the yield of SO4 •- by enhancing electron donating capacity of the reacting system. The degradation products of CP and their acute toxicities suggested that UV305/PDS/TEMPO process has better performance on CP detoxification than UV305/PDS process. This study provides a new way to tackle the challenge of pharmaceutical pollutions in homogeneous photocatalysis process for natural water and sewage restoration.

11.
Appl Catal B ; 317: 121709, 2022 Nov 15.
Article in English | MEDLINE | ID: mdl-35812172

ABSTRACT

Ribavirin (RBV) is an antiviral drug used for treating COVID-19 infection. Its release into natural waters would threaten the health of aquatic ecosystem. This study reports an effective approach to degrade RBV by the trace N-oxyl compounds (2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO) and N-Hydroxyphthalimide (NHPI)) enhanced UV activated free chlorine (UV/Chlorine) process. The results indicated that TEMPO and NHPI at low concentrations (0.1 µM and 1 µM, respectively) could strongly enhance RBV degradation in both deionized water with different pHs and practical surface water. The enhancement was verified to be attributed to the transformation of TEMPO and NHPI into their reactive forms (i.e., TEMPO+ and PINO), which generations deeply relied on radicals. The two N-oxyl compounds inhibit ClO• yield by hindering the reaction of free chlorine vs. HO• and Cl•. The analyses on acute toxicities of RBV degradation products indicate that UV/Chlorine/N-oxyl compounds process can detoxify RBV more efficiently than UV/Chlorine process.

12.
Spectrochim Acta A Mol Biomol Spectrosc ; 259: 119918, 2021 Oct 05.
Article in English | MEDLINE | ID: mdl-33991814

ABSTRACT

Molecular dynamics simulations and DFT calculations were performed for the demonstration of the structural dynamics and vibrational feature of N-Acetyl-d-glucosamine (NAG) in solution phase. The interactions between NAG and solvent molecules were evaluated through spatial distribution function and radial distribution function, and the preferred conformations of NAG in aqueous solution were revealed by cluster analysis. Results from normal mode analysis show that the solvent induced structural fluctuation of NAG could be reflected in the vibrational feature of specific chromophores, thus we can evaluate the molecular structure with the help of its vibrational signature based on the built correlation between molecular structure and vibrational frequencies of specific groups.


Subject(s)
Acetylglucosamine , Glucosamine , Molecular Dynamics Simulation , Vibration , Water
13.
Spectrochim Acta A Mol Biomol Spectrosc ; 247: 119066, 2021 Feb 15.
Article in English | MEDLINE | ID: mdl-33091736

ABSTRACT

Protein's biological function is critically associated with its structural feature, which is encoded in its amino acid sequence. For evaluation of conformational fluctuation and folding mechanism, DFT calculations were performed on the model compound - lysine dipeptide (LYSD) in gas phase to demonstrate the correlation between amide-I vibrations and secondary structure. Molecular dynamics simulations were carried out for the structural dynamics of LYSD in aqueous solution. The results show that LYSD tends form C7eq, C5, ß, PPII and α conformations in the gas phase and primarily presented PPII and α conformations in aqueous solution. The obtained amide-I vibrational frequencies of LYSD conformers were assigned, thus build the correlations between amide-I probes and secondary structure of LYSD. These results provide theoretical insights into the structural feature of LYSD through amide-I vibrations, and would shed light on site specific structural prediction of polypeptides.


Subject(s)
Amides , Dipeptides , Molecular Dynamics Simulation , Lysine , Vibration
14.
ACS Appl Mater Interfaces ; 13(24): 28662-28667, 2021 Jun 23.
Article in English | MEDLINE | ID: mdl-34114811

ABSTRACT

Porous organic frameworks have emerged as the promising platforms to construct tunable microlasers. Most of these microlasers are achieved from metal-organic frameworks via meticulously accommodating the laser dyes with the sacrifice of the pore space, yet they often suffer from the obstacles of either relatively limited gain concentration or sophisticated fabrication techniques. Herein, we reported on the first hydrogen-bonded organic framework (HOF) microlasers with color-tunable performance based on conformation-dependent stimulated emissions. Two types of HOF microcrystals with the same gain lumnogen as the building block were synthesized via a temperature-controlled self-assembly method. The distinct frameworks offer different conformations of the gain building block, which lead to great impacts on their conjugation degrees and excited-state processes, resulting in remarkably distinct emission colors (blue and green). Accordingly, blue/green-color lasing actions were achieved in these two types of HOFs based on well-faceted assembled wire-like cavities. These results offer a deep insight on the exploitation of HOF-based miniaturized lasers with desired nanophotonics performances.

15.
Spectrochim Acta A Mol Biomol Spectrosc ; 227: 117681, 2020 Feb 15.
Article in English | MEDLINE | ID: mdl-31685425

ABSTRACT

The azido asymmetric stretching motion is widely used for the elucidation of the intrinsic conformational preference and folding mechanism of protein since it has strong vibrational absorbance in the spectral transparent windows. However, the possible secondary structural disturbance induced by the insertion of azido group in the side chain of polypeptides should be carefully evaluated. Here, DFT calculation and enhanced sampling method were employed for model dipeptides with or without azido substitution, and the outcome results show that the lower potential energy basins of isolated model dipeptides are consistent with the preferred structural distributions of model dipeptides in aqueous solution. The azido asymmetric stretching frequency shows its sensitivity to the backbone configurations just like amide-I vibration does, and the azido vibration exhibits great potential as a structural reporter in the transparent window. For the evaluation of the application of azido group in biologically related system, the structural dynamics of Aß37-42 and N3-Aß37-42 fragments and the self-assemble process of their protofiliments in aqueous solution were demonstrated. The outcome results show that the structural fluctuations of Aß37-42 and its protofilament in aqueous solution are quite similar with or without azido substitution, and the dewetting transitions of Aß37-42 and N3-Aß37-42 ß-sheet layers are both complete within 30 ns and assemble into stable protofilaments. Therefore, the azido asymmetric vibrational motion is a minimally invasive structural probe and would not introduce much disturbance to the structural dynamics of polypeptides.


Subject(s)
Amyloid beta-Peptides/chemistry , Azides/chemistry , Dipeptides/chemistry , Models, Molecular , Molecular Probes/chemistry , Vibration , Amides/chemistry , Molecular Dynamics Simulation , Protein Structure, Secondary , Solutions , Water/chemistry
16.
J Phys Chem B ; 124(41): 9154-9162, 2020 10 15.
Article in English | MEDLINE | ID: mdl-32965118

ABSTRACT

The specific host-guest interactions in the corresponding complexes of K+ and NH4+ with typical crown ethers were investigated by using FTIR and ultrafast IR spectroscopies. The counteranions, i.e., SCN-, were employed as a local vibrational probe to report the structural dynamics of the complexation. It was found that the vibrational relaxation dynamics of the SCN- was strongly affected by the cations confined in the cavities of the crown ethers. The time constant of the vibrational population decay of SCN- in the complex of NH4+ with the 18-crown-6 was determined to be 6 ± 2 ps, which is ∼30 times faster than that in the complex of K+ with the crown ethers. Control experiments showed that the vibrational population decay of SCN- depended on the size of the cavities of the crown ethers. A theoretical calculation further indicated that the nitrogen atom of SCN- showed preferential coordination to the K+ ions hosted by the crown ethers, while the NH4+ can form hydrogen bonds with the oxygen atoms in the studied crown ethers. The geometric constraints formed in the complex of crown ethers can cause a specific interaction between the NH4+ and SCN-, which can facilitate the intermolecular vibrational energy redistribution of the SCN-.

17.
Chemphyschem ; 10(13): 2242-50, 2009 Sep 14.
Article in English | MEDLINE | ID: mdl-19637206

ABSTRACT

Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L-alpha-glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal-mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by pairwise cross peaks in the femtosecond broadband two-dimensional infrared (2D IR) spectra, which are simulated using time-domain third-order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.


Subject(s)
Cellobiose/chemistry , Guanine/chemistry , Peptides/chemistry , Phosphatidylethanolamines/chemistry , Computer Simulation , Quantum Theory , Spectrophotometry, Infrared
18.
J Phys Chem B ; 113(6): 1681-92, 2009 Feb 12.
Article in English | MEDLINE | ID: mdl-19152255

ABSTRACT

Quantum mechanical computations and molecular dynamics simulations are carried out for the simplest sugar glycolaldehyde to gain insight into the underlying force fields that determine the vibrational spectroscopic parameters relevant to structure and dynamics. The harmonic and anharmonic vibrational frequencies of the 3N--6 modes and their diagonal and off-diagonal anharmonicities are evaluated using the hybrid B3LYP functional in comparison with other high-level theories. Very good performance of B3LYP/6-31+G** is found in predicting the anharmonic frequencies by statistical analysis and by comparison to gas-phase experiments. Full cubic and semidiagonal quartic anharmonic force constants, the origin of the anharmonicities, the isotope dependence of the anharmonicities, and the polarizable continuum solvent effect on the anharmonicities are examined, in particular, for the CO, C-H, and O-H stretching modes. Site-dependent dynamical interactions between glycolaldehyde and water molecules in the hydration shells are examined by molecular dynamics simulations employing a set of molecular mechanical force fields developed on the basis of quantum mechanical computations. The statistical distributions and correlations of the fundamental transition frequencies and transition dipoles are obtained through instantaneous normal-mode analysis. The simultaneous assessment of multiple parameters of multiple vibrational probes shall prove useful in understanding the characteristics of sugar structure and dynamics expressed in two-dimensional infrared correlation spectra.


Subject(s)
Acetaldehyde/analogs & derivatives , Carbohydrates/chemistry , Computer Simulation , Models, Chemical , Quantum Theory , Acetaldehyde/chemistry , Molecular Structure , Solvents/chemistry , Vibration
19.
Phys Chem Chem Phys ; 11(40): 9149-59, 2009 Oct 28.
Article in English | MEDLINE | ID: mdl-19812835

ABSTRACT

A molecular mechanics (MM) force field-based empirical electrostatic potential map (MM map) for amide-I vibrations is developed with the aim of seeking a quick and reasonable approach to computing local mode parameters and their distributions in solution phase. Using N-methylacetamide (NMA) as a model compound, the instantaneous amide-I normal-mode parameters (transition frequency and dipole) obtained at the level of MM force fields are converted to solution phase values by a four-site potential scheme, but without the need for quantum mechanical frequency computations of solute-solvent clusters as are required in constructing ab initio-based electrostatic potential or field maps. The linear IR line shape of the amide-I mode in NMA obtained from the frequency-time correlation function on the basis of the MM map are found to be comparable to those from the ab initio-based maps. Our results show that the amide-I local mode parameters are largely determined by the solvated peptide structure rather than by explicit solvent molecules, suggesting an inherent local structure sensitivity of the amide-I mode in solvated peptides. Applications to alanine di- and tripeptides are satisfactorily demonstrated, showing its usefulness as an alternative approach in providing vibrational parameters for the simulation of linear IR and 2D IR spectra of the amide-I modes in polypeptides.


Subject(s)
Amides/chemistry , Dipeptides/chemistry , Oligopeptides/chemistry , Acetamides/chemistry , Dimethyl Sulfoxide/chemistry , Molecular Dynamics Simulation , Protein Conformation , Solutions , Solvents/chemistry , Spectroscopy, Fourier Transform Infrared
20.
Spectrochim Acta A Mol Biomol Spectrosc ; 219: 391-400, 2019 Aug 05.
Article in English | MEDLINE | ID: mdl-31059891

ABSTRACT

Vibrational spectroscopy has been known as particularly well-suited for deciphering the polypeptide's structure. To decode structural information encoded in IR spectra, we developed amide-I frequency maps on the basis of model dipeptides to correlate the amide-I frequency of interest to the combination of the calculated secondary structure dependent amide-I frequency by using DFT method and the electrostatic potentials that projected onto the amide unit from the micro-environment within molecular mechanics force field. The constructed maps were applied to model dipeptides and amyloid ß-peptide fragment (Aß25-35). The dipeptide specified map (DS map) and the hybrid map (HYB map) predicted amide-I bands of Aß25-35 in solution satisfactorily reproduce experimental observation, and indicate the preference of forming ß-sheet and random coil structure for Aß25-35 in D2O just as the results of cluster analysis suggested. These maps with secondary structural sensitivity and amino acid residue specificity open up a way for the interpretation of amide-I vibrations and show their potentials in the understanding of molecular structure of polypeptides in solution.


Subject(s)
Amyloid beta-Peptides/chemistry , Dipeptides/chemistry , Peptide Fragments/chemistry , Amides/chemistry , Humans , Molecular Dynamics Simulation , Protein Structure, Secondary , Spectrophotometry, Infrared , Static Electricity , Water/chemistry
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