Displaying all 18 publications

  1. Misran O, Timimi BA, Heidelberg T, Sugimura A, Hashim R
    J Phys Chem B, 2013 Jun 20;117(24):7335-44.
    PMID: 23718628 DOI: 10.1021/jp401787b
    We have investigated the phase behavior of four glycosides (βC8OGlc, βC8SGlc, βC10OGlc, βC8OGal) in water and D2O by optical polarizing microscopy and deuterium NMR. Previously published phase diagrams were evaluated by deuterium NMR, via monitoring D2O spectra, and confirmed the presence of the hexagonal, bicontinuous cubic, and lamellar phases in these glycosides. We have also shown the presence of the gel phase in (βC10OGlc) and observed the extensive supercooling of the lamellar phase to temperatures well below the Kraft line. While the main features of the phase diagrams were confirmed, some phase boundaries were found to be slightly different. Magnetically aligned spectra were also observed for relatively dilute samples for the hexagonal phase (βC8OGlc and βC8OGal) and the lamellar phase (βC8SGlc and βC10OGlc). The average number of bound water molecules per headgroup in the lamellar phase for the glycosides was determined by the systematic measurement of the quadrupolar splitting of D2O over a wide range of values of the (glycoside/water) molar ratio. The number of water molecules bound to the headgroup was found on average to be about 1.6-1.7 water molecules with no significant differences in this value for the different glycosides (and over the temperature range investigated), indicating that the bound water content is predominately influenced by the number of hydroxyl groups of the headgroup only. However, this bound water content of only 1.6-1.7 water molecules per sugar headgroup is surprisingly low, suggesting strong intermolecular interactions of the OH groups of headgroup sugars. The results are in line with computational results reported earlier for the octyl-β-glucoside and β-galactoside, which show the presence of strong intralayer hydrogen bonding.
  2. Achari VM, Nguan HS, Heidelberg T, Bryce RA, Hashim R
    J Phys Chem B, 2012 Sep 27;116(38):11626-34.
    PMID: 22967067
    Glycolipids form materials of considerable potential for a wide range of surfactant and thin film applications. Understanding the effect of glycolipid covalent structure on the properties of their thermotropic and lyotropic assemblies is a key step toward rational design of new glycolipid-based materials. Here, we perform molecular dynamics simulations of anhydrous bilayers of dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside, and a C(12)C(10) branched β-maltoside. Specifically, we examine the consequences of chain branching and headgroup identity on the structure and dynamics of the lamellar assemblies. Chain branching of the glycolipid leads to measurable differences in the dimensions and interactions of the lamellar assembly, as well as a more fluid-like hydrophobic chain region. Substitution of the maltosyl headgroup of βMal-C(12) by an isomaltosyl moiety leads to a significant decrease in bilayer spacing as well as a markedly altered pattern of inter-headgroup hydrogen bonding. The distinctive simulated structures of the two regioisomers provide insight into the difference of ~90 °C in their observed clearing temperatures. For all four simulated glycolipid systems, with the exception of the sn-2 chain of the branched maltoside, the alkyl chains are ordered and exhibit a distinct tilt, consistent with recent crystallographic analysis of a branched chain Guerbet glycoside. These insights into structure-property relationships from simulation provide an important molecular basis for future design of synthetic glycolipid materials.
  3. Yusof NS, Khan MN
    J Phys Chem B, 2012 Feb 23;116(7):2065-74.
    PMID: 22272582 DOI: 10.1021/jp210467p
    The semiempirical kinetic method has been used to determine the ratio of cetyltrimethylammonium bromide, CTABr, micellar binding constants of counterions X (K(X)) and Br (K(Br)), i.e., K(X)/K(Br) (= R(X)(Br)) for X = dianionic 5-methyl- and 5-methoxysalicylate ions. The values of K(X) and K(Br) have been derived from the kinetic parameters obtained in the presence of spherical/nonspherical and spherical micelles, respectively. The values of R(X)(Br) remain essentially independent of [CTABr] within its range 0.005-0.015 M for both dianionic 5-methyl- and 5-methoxysalicylate ions. The increase in temperature from 35 to 55 °C decreases the values of R(X)(Br) from 796 to 53 for 5-methylsalicylate ions and from 89 to 7.0 for 5-methoxysalicylate ions. Rheological properties of 0.015 M CTABr solutions containing ≥0.01 M counterionic salt, M(2)X, show indirectly the presence of unilamellar vesicles, ULV, and long linear, entangled, and branched wormlike micelles, WM, at, respectively, 35 and 55 °C for X = dianionic 5-methylsalicylate ion. However, such studies show WM and probable spherical micelles, SM, at, respectively, 35 and 55 °C for X = dianionic 5-methoxysalicylate ions. It has been shown that, at a constant [CTABr], the micellar structural transitions from SM-to-WM-to-vesicles may be correlated quantitatively with the values of R(X)(Br) regardless of whether such micellar structural transitions occur due to variation in the values of [M(2)X] at a constant temperature or due to variation in temperature at a constant [M(2)X].
  4. Khan MN, Azri MH
    J Phys Chem B, 2010 Jun 24;114(24):8089-99.
    PMID: 20509705 DOI: 10.1021/jp102109q
    Pseudofirst-order rate constants for aqueous cleavage of N-(2'-hydroxyphenyl)phthalimide (1), obtained at 0.001 M NaOH, 2 x 10(-4) M 1, 2% v/v CH(3)CN, and 30 degrees C, show a nonmonotonic decrease with the increase in the total concentration of cetyltrimethylammonium bromide ([CTABr](T)) within its range >/=9 x 10(-5)-or=0.04 M CTABr and within a [NaBr] range of 0.0-0.005 M. These observations, in view of the pseudophase (PP) model of the micelle, reveal the presence of presumably spherical micelles at or=4 x 10(-4) M causes a micellar structural transition from most likely spherical to cylindrical, which is evident from the increase in K(S) values from 3.46 x 10(3) to 11.4 x 10(3) M(-1) with the increase in [CTABr](T) from 4 x 10(-4) to approximately 1 x 10(-3) M in the absence of NaBr. The values of k(obs) at different [NaBr] and at a constant [CTABr](T) follow a kinetic relationship derived from an empirical equation coupled with a PP model of micelle. This relationship gives the value of a kinetic parameter, F(X/S), which represents the fraction of micellized S(-) (S(-) = 1(-)) transferred to the aqueous phase by the limiting concentration of X(-) (X(-) = Br(-)) through ion exchange X(-)/S(-). The value of F(Br/1) is 0.65 +/- 0.12.
  5. Cheong MY, Ariffin A, Khan MN
    J Phys Chem B, 2007 Oct 25;111(42):12185-94.
    PMID: 17914797
    Pseudo-first-order rate constants (k(obs)) for alkaline hydrolysis of N-benzylphthalimide (1) show a nonlinear decrease with the increase in [C(m)E(n)]T (total concentration of Brij 58, m = 16, n = 20 and Brij 56, m = 16, n = 10) at constant [CH(3)CN] and [NaOH]. These nonionic micellar effects, within the certain typical reaction conditions, have been explained in terms of the pseudophase micellar (PM) model. The values of micellar binding constants (KS) of 1 are 1.04 x 10(3) M(-1) (at 1.0 x 10(-3) M NaOH) and 1.08 x 10(3) M(-1) (at 2.0 x 10(-3) M NaOH) for C(16)E(20) as well as 600 M(-1) (at 7.6 x 10(-4) M NaOH) and 670 M(-1) (at 1.0 x 10(-3) M NaOH) for C(16)E(10) micelles. The pseudo-first-order rate constants (kM) for hydrolysis of 1 in C(16)E(20) micellar pseudophase are approximately 90-fold smaller than those (kW) in water phase. The values of kM for hydrolysis of 1 in C(16)E(10) micelles are almost zero. Kinetic coupled with UV spectral data reveals significant irreversible nonionic micellar binding of 1 molecules in the micellar environment of nearly zero hydroxide ion concentration at >or=0.14 M C(16)E(20) and 1.0 x 10(-3) M NaOH while such observations could not be detected at or=3 x 10(-3) M C(16)E(10) and 7.6 x 10(-4) M NaOH, while the rate of hydrolysis of 1 is completely ceased at >or=0.05 M C(16)E(10) and 7.6 x 10(-4) M NaOH. The rate of hydrolysis of 1 at 5.0 x 10(-2) and 8.8 x 10(-2) M C(16)E(10) and 1.0 x 10(-3) M NaOH reveals the formation of presumably phthalic anhydride, whereas such observation was not observed in the C(16)E(20) micellar system under similar experimental conditions.
  6. Chong TT, Hashim R, Bryce RA
    J Phys Chem B, 2006 Mar 16;110(10):4978-84.
    PMID: 16526739
    Comparative molecular dynamics simulations of n-octyl-beta-D-galactopyranoside (beta-C8Gal) and n-octyl-beta-D-glucopyranoside (beta-C8Glc) micelles in aqueous solution have been performed to explore the influence of carbohydrate stereochemistry on glycolipid properties at the atomic level. In particular, we explore the hypothesis that differences in T(m) and T(c) for beta-C8Gal and beta-C8Glc in lyotropic systems arise from a more extensive hydrogen bonding network between beta-C8Gal headgroups relative to beta-C8Glc, due to the axial 4-OH group in beta-C8Gal. Good agreement of the 13 ns micelle-water simulations with available experimental information is found. The micelles exhibit a similar shape, size, and degree of exposed alkyl chain surface area. We find net inter- and intra-headgroup hydrogen bonding is also similar for beta-C8Gal and beta-C8Glc, although n-octyl-beta-D-galactopyranoside micelles do exhibit a slightly greater degree of inter- and intra-headgroup hydrogen bonding. However, the main distinction in the calculated microscopic behavior of beta-C8Glc and beta-C8Gal micelles lies in solvent interactions, where beta-d-glucosyl headgroups are considerably more solvated (mainly at the equatorial O4 oxygen). These results agree with preceding theoretical and experimental studies of monosaccharides in aqueous solution. A number of long water residence times are found for solvent surrounding both micelle types, the largest of which are associated with surface protrusions involving headgroup clusters. Our simulations, therefore, predict differences in hydrogen bonding for the two headgroup stereochemistries, including a small difference in inter-headgroup interactions, which may contribute to the higher T(m) and T(c) values of beta-C8Gal surfactants relative to beta-C8Glc in lyotropic systems.
  7. Brela MZ, Wójcik MJ, Witek ŁJ, Boczar M, Wrona E, Hashim R, et al.
    J Phys Chem B, 2016 04 28;120(16):3854-62.
    PMID: 27045959 DOI: 10.1021/acs.jpcb.6b01601
    In this study, the proton dynamics of hydrogen bonds for two forms of crystalline aspirin was investigated by the Born-Oppenheimer molecular dynamics (BOMD) method. Analysis of the geometrical parameters of hydrogen bonds using BOMD reveals significant differences in hydrogen bonding between the two crystalline forms of aspirin, Form I and Form II. Analysis of the trajectory for Form I shows spontaneous proton transfer in cyclic dimers, which is absent in Form II. Quantization of the O-H stretching modes allows a detailed discussion on the strength of hydrogen-bonding interactions. The focal point of our study is examination of the hydrogen bond characteristics in the crystal structure and clarification of the influence of hydrogen bonding on the presence of the two crystalline forms of aspirin. In the BOMD method, thermal motions were taken into account. Solving the Schrödinger equation for the snapshots of 2D proton potentials, extracted from MD, gives the best agreement with IR spectra. The character of medium-strong hydrogen bonds in Form I of aspirin was compared with that of weaker hydrogen bonds in aspirin Form II. Two proton minima are present in the potential function for the hydrogen bonds in Form I. The band contours, calculated by using one- and two-dimensional O-H quantization, reflect the differences in the hydrogen bond strengths between the two crystalline forms of aspirin, as well as the strong hydrogen bonding in the cyclic dimers of Form I and the medium-strong hydrogen bonding in Form II.
  8. Khyasudeen MF, Nowakowski PJ, Tan HS
    J Phys Chem B, 2019 02 14;123(6):1359-1364.
    PMID: 30657672 DOI: 10.1021/acs.jpcb.9b00099
    We use two-dimensional electronic spectroscopy to measure the ultrafast correlation dynamics between the Q x and Q y transitions in chlorophyll molecules. We derive a variation to the center line slope method to quantify the frequency fluctuation cross-correlation function, C xy( Tw). Compared with the frequency fluctuation correlation function of the Q y transition, we observe that there is only a minimal correlation between the Q x and Q y transition, even at the ultrashort timescale of ∼100 fs, which then decays to zero in a time scale of ∼2 ps.
  9. Maidur SR, Patil PS, Katturi NK, Soma VR, Ai Wong Q, Quah CK
    J Phys Chem B, 2021 Apr 22;125(15):3883-3898.
    PMID: 33830758 DOI: 10.1021/acs.jpcb.1c01243
    The structural, thermal, linear, and femtosecond third-order nonlinear optical (NLO) properties of two pyridine-based anthracene chalcones, (2E)-1-(anthracen-9-yl)-3-(pyridin-2-yl)prop-2-en-1-one (2PANC) and (2E)-1-(anthracen-9-yl)-3-(pyridin-3-yl)prop-2-en-1-one (3PANC), were investigated. These two chalcones were synthesized following the Claisen-Schmidt condensation method. Optically transparent single crystals were achieved using a slow evaporation solution growth technique. The presence of functional groups in these molecules was established by Fourier transform infrared and NMR spectroscopic data. The detailed solid-state structure of both chalcones was determined from the single-crystal X-ray diffraction data. Both crystals crystallized in the centrosymmetric triclinic space group P1̅ with the nuance of unit cell parameters. The crystals (labeled as 2PANC and 3PANC) have been found to be transparent optically [in the entire visible spectral region] and were found to be thermally stable up to 169 and 194 °C, respectively. The intermolecular interactions were investigated using the Hirshfeld surface analysis, and the band structures (highest occupied molecular orbital-lowest unoccupied molecular orbital, excited-state energies, global chemical reactivity descriptors, and molecular electrostatic potentials) were studied using density functional theory (DFT) techniques. The ultrafast third-order NLO properties were investigated using (a) Z-scan and (b) degenerate four-wave mixing (DFWM) techniques using ∼50 fs pulses at 800 nm (1 kHz, ∼4 mJ) from a Ti:sapphire laser amplifier. Two-photon-assisted reverse saturable absorption, self-focusing nonlinear refraction, optical limiting, and optical switching behaviors were witnessed from the Z-scan data. 3PANC demonstrated a stronger two-photon absorption coefficient, while 2PANC depicted a stronger nonlinear refractive index among the two. The time-resolved DFWM data demonstrated that the decay times of 2PANC and 3PANC were ∼162 and ∼180 fs, respectively. The second hyperpolarizability (γ) values determined by DFT, Z-scan, and DFWM were found to be in good correlation (with a magnitude of ∼10-34 esu). The ultrafast third-order NLO response, significant NLO properties, and thermal stability of these chalcones brands them as potential candidates for optical power limiting and switching applications.
  10. Wan Iskandar WFN, Salim M, Patrick M, Timimi BA, Zahid NI, Hashim R
    J Phys Chem B, 2021 05 06;125(17):4393-4408.
    PMID: 33885309 DOI: 10.1021/acs.jpcb.0c10629
    The lyotropic phase behavior of four common and easily accessible glycosides, n-octyl α-d-glycosides, namely, α-Glc-OC8, α-Man-OC8, α-Gal-OC8, and α-Xyl-OC8, was investigated. The presence of normal hexagonal (HI), bicontinuous cubic (VI), and lamellar (Lα) phases in α-Glc-OC8 and α-Man-OC8 including their phase diagrams in water reported previously was verified by deuterium nuclear magnetic resonance (2H NMR), via monitoring the D2O spectra. Additionally, the partial binary phase diagrams and the liquid crystal structures formed by α-Gal-OC8 and α-Xyl-OC8 in D2O were constructed and confirmed using small- and wide-angle X-ray scattering and 2H NMR. The average number of bound water molecules (nb) per headgroup in the Lα phase was determined by the systematic measurement of the quadrupolar splitting of D2O over a wide range of molar ratio values (glycoside/D2O), especially at high glucoside composition. The number of bound water molecules bound to the headgroup was found to be around 1.5-2.0 for glucoside, mannoside, and galactoside, all of which possesses four OH groups. In the case of xyloside, which has only three OH groups, the bound water content is ∼2.0. Our findings confirmed that the bound water content of all n-octyl α-d-glycosides studied is lower compared to the number of possible hydrogen bonding sites possibly due to the fact that most of the OH groups are involved in intralayer interaction that holds the lipid assembly together.
  11. Tuan Kob TNA, Ismail MF, Abdul Rahman MB, Cordova KE, Mohammad Latif MA
    J Phys Chem B, 2020 05 07;124(18):3678-3685.
    PMID: 32275422 DOI: 10.1021/acs.jpcb.0c02145
    Herein, we detail an atomic-level investigation of the cutinase enzyme encapsulated within a model metal-organic framework (MOF) platform using quantum mechanics calculations and molecular dynamics simulations. Cutinase, when encapsulated in an isoreticularly expanded MOF-74 (cutinase@IRMOF-74-VI), was proven to maintain its structural stability at temperatures that would otherwise denature the enzyme in its unprotected native state. Hydrogen bonding and salt bridge interactions, most notably involving arginine residues at the surface of the enzyme, were critical for stabilizing cutinase within the pore channels of IRMOF-74-VI. The findings reported support the viability of enzyme encapsulation in a porous material by demonstrating that a model enzyme not only retains its structural integrity but also remains accessible and active under extreme and foreign conditions.
  12. Mbous YP, Hayyan M, Wong WF, Hayyan A, Looi CY, Hashim MA
    J Phys Chem B, 2020 10 15;124(41):9086-9094.
    PMID: 32930594 DOI: 10.1021/acs.jpcb.0c04801
    Deep eutectic solvent (DES) affinities with cellular membranes structures dictate the degree of cytotoxicity that results from these interactions. The physicochemical properties of choline chloride (ChCl)-DESs suggest non-negligible cytotoxicities that were attested by published researches. In this study, the profiles of novel N,N-diethylammonium chloride (DAC)-based-deep eutectic solvents (DESs) prepared with various hydrogen bond donors (urea, glycerol, ethylene glycol, malonic acid, and zinc chloride) were compared to those of ChCl-DESs by using HelaS3, AGS, MCF-7, and WRL-68 cancer cell lines. The molecular interactions between salts and cellular membranes were investigated to explain the observed cytotoxicity. The results show that ChCl-based DESs (279 ≤ IC50 ≥ 1260 mM) were less toxic than DAC-based DESs (37 ≤ IC50 ≥ 109 mM). COSMO-RS analysis emphasized the importance of salt hydrophobicity with regards to DESs cytotoxicity. Malonic acid increased hydrophobicity and cytotoxicity in general, thus highlighting the potential of ammonium salt-based DESs as anticancer agents.
  13. Ramlli MA, Isa MI
    J Phys Chem B, 2016 11 10;120(44):11567-11573.
    PMID: 27723333
    Fourier transform infrared (FT-IR), X-ray diffraction (XRD), and transference number measurement (TNM) techniques were applied to investigate the complexation, structural, and ionic transport properties of and the dominant charge-carrier species in a solid biopolymer electrolyte (SBE) system based on carboxymethyl cellulose (CMC) doped with ammonium fluoride (NH4F), which was prepared via a solution casting technique. The SBEs were partially opaque in appearance, with no phase separation. The presence of interactions between the host polymer (CMC) and the ionic dopant (NH4F) was proven by FT-IR analysis at the C-O band. XRD spectra analyzed using Origin 8 software disclose that the degree of crystallinity (χc%) of the SBEs decreased with the addition of NH4F, indicating an increase in the amorphous nature of the SBEs. Analysis of the ionic transport properties reveals that the ionic conductivity of the SBEs is dependent on the ionic mobility (μ) and diffusion of ions (D). TNM analysis confirms that the SBEs are proton conductors.
  14. Toledo Hijo AA, Maximo GJ, Costa MC, Cunha RL, Pereira JF, Kurnia KA, et al.
    J Phys Chem B, 2017 04 13;121(14):3177-3189.
    PMID: 28332847 DOI: 10.1021/acs.jpcb.7b01384
    Protic ionic liquids (PILs) have emerged as promising compounds and attracted the interest of the industry and the academy community, due to their easy preparation and unique properties. In the context of green chemistry, the use of biocompounds, such as fatty acids, for their synthesis could disclose a possible alternative way to produce ILs with a low or nontoxic effect and, consequently, expanding their applicability in biobased processes or in the development of bioproducts. This work addressed efforts to a better comprehension of the complex solid-[liquid crystal]-liquid thermodynamic equilibrium of 20 new PILs synthesized by using fatty acids commonly found in vegetable oils, as well as their rheological profile and self-assembling ability. The work revealed that their phase equilibrium and physical properties are significantly impacted by the structure of the ions used for their synthesis. The use of unsaturated fatty acids and bis(2-hydroxyethyl)ammonium for the synthesis of these biobased ILs led to a drastic decreasing of their melting temperatures. Also, the longest alkyl chain fatty acids promoted higher self-assembling and more stable mesophases. Besides their sustainable appeal, the marked high viscosity, non-Newtonian profile, and very low critical micellar concentration values of the PIL crystals here disclosed make them interesting renewable compounds with potential applications as emulsifiers, stabilizers, thickeners, or biolubricants.
  15. Parra-Cruz R, Jäger CM, Lau PL, Gomes RL, Pordea A
    J Phys Chem B, 2018 09 13;122(36):8526-8536.
    PMID: 30114369 DOI: 10.1021/acs.jpcb.8b05926
    The stability of enzymes is critical for their application in industrial processes, which generally require different conditions from the natural enzyme environment. Both rational and random protein engineering approaches have been used to increase stability, with the latter requiring extensive experimental effort for the screening of variants. Moreover, some general rules addressing the molecular origin of protein thermostability have been established. Herein, we demonstrate the use of molecular dynamics simulations to gain molecular level understanding of protein thermostability and to engineer stabilizing mutations. Carbonic anhydrase (CA) is an enzyme with a high potential for biotechnological carbon capture applications, provided it can be engineered to withstand the high temperature process environments, inevitable in most gas treatment units. In this study, we used molecular dynamics simulations at 343, 353, and 363 K to study the relationship between structure flexibility and thermostability in bacterial α-CAs and applied this knowledge to the design of mutants with increased stability. The most thermostable α-CA known, TaCA from Thermovibrio ammonificans, had the most rigid structure during molecular dynamics simulations, but also showed regions with high flexibility. The most flexible amino acids in these regions were identified from root mean square fluctuation (RMSF) studies, and stabilizing point mutations were predicted based on their capacity to improve the calculated free energy of unfolding. Disulfide bonds were also designed at sites with suitable geometries and selected based on their location at flexible sites, assessed by B-factor calculation. Molecular dynamics simulations allowed the identification of five mutants with lower RMSF of the overall structure at 400 K, compared to wild-type TaCA. Comparison of free-energy landscapes between wild-type TaCA and the most promising mutants, Pro165Cys-Gln170Cys and Asn140Gly, showed an increased conformational stability of the mutants at 400 K.
  16. Carr AC, Piunova VA, Maarof H, Rice JE, Swope WC
    J Phys Chem B, 2018 05 31;122(21):5356-5367.
    PMID: 29385796 DOI: 10.1021/acs.jpcb.7b10539
    We present an all-atom molecular dynamics study of the effect of a range of organic solvents (dichloromethane, diethyl ether, toluene, methanol, dimethyl sulfoxide, and tetrahydrofuran) on the conformations of a nanogel star polymeric nanoparticle with solvophobic and solvophilic structural elements. These nanoparticles are of particular interest for drug delivery applications. As drug loading generally takes place in an organic solvent, this work serves to provide insight into the factors controlling the early steps of that process. Our work suggests that nanoparticle conformational structure is highly sensitive to the choice of solvent, providing avenues for further study as well as predictions for both computational and experimental explorations of the drug-loading process. Our findings suggest that when used in the drug-loading process, dichloromethane, tetrahydrofuran, and toluene allow for a more extensive and increased drug-loading into the interior of nanogel star polymers of the composition studied here. In contrast, methanol is more likely to support shallow or surface loading and, consequently, faster drug release rates. Finally, diethyl ether should not work in a formulation process since none of the regions of the nanogel star polymer appear to be sufficiently solvated by it.
  17. Jana S, Do TN, Nowakowski PJ, Khyasudeen MF, Le DV, Lim IJY, et al.
    J Phys Chem B, 2023 Aug 24;127(33):7309-7322.
    PMID: 37579317 DOI: 10.1021/acs.jpcb.3c02521
    In a two-dimensional (2D) optical spectrum of a multilevel system, there are diagonal peaks and off-diagonal cross-peaks that correlate the different levels. The time-dependent properties of these diagonal peaks and cross-peaks contain much information about the dynamics of the multilevel system. The time-dependent diagonal peakshape that depends on the spectral diffusion dynamics of the associated transition and characterized by the frequency-fluctuation correlation function (FFCF) is well studied. However, the time-dependent peakshape of a cross-peak that provides the correlation dynamics between different transitions is much less studied or understood. We derived the third-order nonlinear response functions that describe the cross-peaks in a 2D electronic spectrum of a multilevel system that arise from processes sharing a common ground state and/or from internal conversion and population transfer. We can use the center line slope (CLS) analysis to characterize the cross-peaks in conjunction with the diagonal peaks. This allows us to recover the frequency-fluctuation cross-correlation functions (FXCFs) between two transitions. The FXCF and its subsidiary quantities such as the initial correlation and the initial covariance between different transitions are important for studying the correlation effects between states in complex systems, such as energy-transfer processes. Furthermore, knowledge of how various molecular processes over different timescales affect simultaneously different transitions can also be obtained from the measured FXCF. We validated and tested our derived equations and analysis process by studying, as an example, the 2D electronic spectra of metal-free phthalocyanine in solution. We measured and analyzed the diagonal peaks of the Qx and Qy transitions and the cross-peaks between these two transitions of this multilevel electronic system and obtained the associated FFCFs and FXCFs. In this model system, we measured negative components of FXCF over the tens of picosecond timescale. This suggests that in phthalocyanine, the Qx and Qy transitions coupling with the solvent molecule motion are anticorrelated to each other.
  18. Sanachai K, Mahalapbutr P, Sanghiran Lee V, Rungrotmongkol T, Hannongbua S
    J Phys Chem B, 2021 Dec 23;125(50):13644-13656.
    PMID: 34904832 DOI: 10.1021/acs.jpcb.1c07060
    Global public health has been a critical problem by the sudden increase of the COVID-19 outbreak. The papain-like protease (PLpro) of SARS-CoV-2 is a key promising target for antiviral drug development since it plays a pivotal role in viral replication and innate immunity. Here, we employed the all-atom molecular dynamics (MD) simulations and binding free energy calculations based on MM-PB(GB)SA and SIE methods to elucidate and compare the binding behaviors of five inhibitors derived from peptidomimetic inhibitors (VIR250 and VIR251) and naphthalene-based inhibitors (GRL-0617, compound 3, and compound Y96) against SARS-CoV-2 PLpro. The obtained results revealed that all inhibitors interacting within the PLpro active site are mostly driven by vdW interactions, and the hydrogen bond formation in residues G163 and G271 with peptidomimetics and the Q269 residue with naphthalene-based inhibitors was essential for stabilizing the protein-ligand complexes. Among the five studied inhibitors, VIR250 exhibited the most binding efficiency with SARS-CoV-2 PLpro, and thus, it was chosen for the rational drug design. Based on the computationally designed ligand-protein complexes, the replacement of aromatic rings including heteroatoms (e.g., thiazolopyridine) at the P2 and P4 sites could help to improve the inhibitor-binding efficiency. Furthermore, the hydrophobic interactions with residues at P1-P3 sites can be increased by enlarging the nonpolar moieties (e.g., ethene) at the N-terminal of VIR250. We expect that the structural data obtained will contribute to the development of new PLpro inhibitors with more inhibitory potency for COVID-19.
Related Terms
Contact Us

Please provide feedback to Administrator (afdal@afpm.org.my)

External Links