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To explore the hepatic toxicity and the exposure biomarkers of N, N-Dimethylacetamide.One hundred forty five objects were chosen by stratified random sampling method. The investigation was performed u...Read More
Infrared (IR) spectroscopy of the amide I band has been widely utilized for the analysis of peptides and proteins. Theoretical modeling of IR spectra of proteins requires an accurate and efficient des...Read More
The less polar π-surface of protein amide groups is exposed in many receptor binding sites, either as part of the backbone or in Gln/Asn side chains. Using quantum chemical calculations and Protein D...Read More
The importance of genetic resource preservation has been highlighted in the literature as a means of maintaining genetic diversity. Among the various methods of preserving such resources, semen cryopr...Read More
A new peptidomimetic is proposed, resulting from substitution of the C═O carbonyl group by a B-F bond at the amide linkage. The effects of such chemical alteration are theoretically investigated thr...Read More
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: influence on the folding properties of two beta-peptides in methanol.
Considering N-methylacetamide (NMA) as a model compound, new interaction parameters are developed for the amide function in the GROMOS force field that are compatible with the recently derived 53A6(OX...Read More
Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes.
IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an I...Read More
Estimating the carbonyl anharmonic vibrational frequency from affordable harmonic frequency calculations.
A linear correlation between harmonic and anharmonic frequencies of water calculated at B3LYP level of theory was observed with a number of basis sets. Similar relationships were found in both the gas...Read More
We report high-resolution (0.05 cm(-1)) FTIR spectra of the fundamental and first overtone of the amide I mode of trans-N-methylacetamide (NMA) trapped in solid molecular hydrogen (SMH) at cryogenic t...Read More
Effect of water on solvation structure and dynamics of ions in the peptide bond environment: importance of hydrogen bonding and dynamics of the solvents.
The solvation structure and dynamics of ions in aqueous N-methylacetamide (NMA) solutions are calculated using classical molecular dynamics simulations. Our results are analyzed in terms of varying co...Read More
Effects of peptide backbone amide-to-ester bond substitution on the cleavage frequency in electron capture dissociation and collision-activated dissociation.
Probing the mechanism of electron capture dissociation on variously modified model peptide polycations has resulted in discovering many ways to prevent or reduce N-Cα bond fragmentation. Here we repo...Read More
Effects of the position and manner of hydration on the stability of solvated N-methylacetamides and the strength of binding between N-methylacetamide and water clusters: a computational study.
This work mainly studies the effects of the position (there are two possible hydrated sites) and the manner (i.e., whether water acts as a proton donor or acceptor) of hydration by various numbers of ...Read More
Effect of temperature and pressure on the structure, dynamics, and hydrogen bond properties of liquid N-methylacetamide: a molecular dynamics study.
The structure and dynamical properties of liquid N-methylacetamides (NMA) are calculated at five different temperatures and at four different pressures using classical molecular dynamics simulations. ...Read More
A portable intermolecular potential for molecular dynamics studies of NMA-NMA and NMA-H2O aggregates.
A recently formulated intermolecular potential has been adapted to describe the interaction of the N-methylacetamide (NMA) dimer and of the NMA-H(2)O adduct. The pure electrostatic component of the in...Read More
Modeling the vibrational dynamics and nonlinear infrared spectra of coupled amide I and II modes in peptides.
The amide vibrational modes play an important role in energy transport and relaxation in polypeptides and proteins and provide us with spectral markers for structure and structural dynamics of these m...Read More
Anharmonic overtone and combination states of glycine and two model peptides examined by vibrational self-consistent field theory.
In this paper, the application of the vibrational self-consistent field (VSCF) and correction-corrected VSCF methods for calculating anharmonic parameters, including transition frequency, transition i...Read More
For spectroscopic studies of peptide and protein thermal denaturation it is important to single out the contribution of the solvent to the spectral changes from those originated in the molecular struc...Read More
Molecular dynamics simulations and instantaneous normal-mode analysis of the vibrational relaxation of the C-H stretching modes of N-methylacetamide-d in liquid deuterated water.
Nonequilibrium molecular dynamics (MD) simulations and instantaneous normal mode (INMs) analyses are used to study the vibrational relaxation of the C-H stretching modes (ν(s)(CH?)) of deuterated N-m...Read More
Intermolecular charge flux as the origin of infrared intensity enhancement upon halogen-bond formation of the peptide group.
The changes in the vibrational properties of the peptide group upon formation of O...X and N...X halogen bonds are studied theoretically. Calculations are carried out for complexes of N-methylacetamid...Read More
The natural and fundamental proclivities of interaction between a pair of peptide units are examined using high-level ab initio calculations. The NH···O H-bonded structure is found to be the most s...Read More
Salting effects on protein components in aqueous NaCl and urea solutions: toward understanding of urea-induced protein denaturation.
The mechanism of urea-induced protein denaturation is explored through studying the salting effect of urea on 14 amino acid side chain analogues, and N-methylacetamide (NMA) which mimics the protein b...Read More
A method is proposed to analyze the intra- and intermolecular vibrational energy flow occurring in biomolecules in solution during relaxation processes. It is based on the assumption that the total en...Read More
An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints.
In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in whic...Read More
We studied the pathways of vibrational energy relaxation of the amide I (~1660 cm?1) and amide II (~1560 cm?1) vibrational modes of N-methylacetamide (NMA) in CCl? solution using two-color femtosecond...Read More
Most current biomolecular simulations are based on potential energy functions that treat the electrostatic energy as a sum of pairwise Coulombic interactions between effective fixed atomic charges. Th...Read More