Particle rearrangements during transitions between local minima of the potential energy landscape of a binary Lennard-Jones liquid

The potential energy landscape (PEL) of binary Lennard-Jones (BLJ) mixtures exhibits local minima, or inherent structures (IS), which are organized into metabasins (MBs). We study the particle rearrangements related to transitions between both successive IS and successive MB for a small 80:20 BLJ system near the mode-coupling temperature TMCT. The analysis includes the displacements of individual particles, the localization of the rearrangements, and the relevance of string-like motion. We find that the particle rearrangements during IS and MB transitions do not change significantly at TMCT. In particular, an onset of single particle hopping on the length scale of the interparticle distance is not observed. Further, it is demonstrated that IS and MB dynamics are spatially heterogeneous and facilitated by string-like motion. To investigate the mechanism of string-like motion, we follow the particle rearrangements during suitable sequences of IS transitions. We find that most strings observed after a series of transitions do not move coherently during a single transition, but subunits of different sizes are active at different times. Several findings suggest that, though string-like motion is of comparable relevance when the system explores a MB and when it moves from one MB to another, the occurrence of a successful string enables the system to exit a MB. Moreover, we show that the particle rearrangements during two consecutive MB transitions are basically uncorrelated. In particular, different groups of particles are highly mobile. We further find the positions of strings during successive MB transitions weakly but positively correlated, supporting the idea of dynamic facilitation. Finally, the relation between the features of the potential energy landscape and the relaxation processes in supercooled liquids is discussed.     

Raman study of structural relaxation and boson peak in amorphous films of adamantane

Low-frequency Raman scattering was used to study amorphous solid films of adamantane, a globular non-polar hydrocarbon molecule. As evidenced by its spectral characteristics this type of disorder is different from the orientational disorder found in the room temperature plastic phase by the absence of the translational order as well. This gives rise to the boson peak related to acoustic phonons which gradually disappears upon heating with simultaneous emerging of the phonon line at 50 cm-1 which characterizes the low-temperature ordered phase of adamantane. Adamantane dynamics resembles that of C60 fullerene although not in the same temperature range. All this makes adamantane an attractive system that could serve as a practical reference in molecular simulation studies of the glassy phase of model fluids.     

Damping of sound waves in the terahertz range and strength of the boson peak

By applying a new two-step line-shape analysis to inelastic neutron and x-ray scattering spectra of glassy systems, we were able to resolve the acoustic excitations from the low-frequency excess modes and to accurately estimate the damping of sound waves in the terahertz frequency range. Using this approach, we estimated the damping parameter for terahertz acoustic waves in a wide class of chemically different glasses and did a quantitative comparison of the results with prediction of theoretical models. By comparing the estimates of the mean-free path of the acoustic modes in different glasses and the corresponding boson peak strengths, we show the existence of a simple correlation between these two quantities. The relationship between attenuation of the terahertz acoustic modes, strength of the boson peak, and fragility is discussed.     

Shear-induced disappearances of energy minima and plastic deformation in polymer glasses

The potential energy landscape of a polymer glass is examined with regard to plastic deformation under shear strain. Shear strain is found to cause the disappearance of local potential energy minima, as determined by the decrease to zero of the curvature of the local minima. If the local energy minimum which the system is in disappears, the system becomes mechanically unstable and is forced to relax to an alternate energy minimum. This mechanical instability, which leads to a discontinuous change in system properties, is inherently irreversible—the new local minimum will not disappear, in general, when the strains are reversed. These disappearances of local energy minima and the associated irreversible relaxations lead to plastic deformation in polymer glasses.     

Antibacterial thymol derivatives isolated from Centipeda minima

Two new monoterpenoids, 8,10-dihydroxy-9(2)-methylbutyryloxythymol (1) and 10-hydroxy-8,9-dioxyisopropylidene-thymol (2), together with five known thymol derivatives: 8,9,10-trihydroxythymol (3), thymol-beta-glucopyranoside (4), 9-hydroxythymol (5), 8,10-dihydroxy-9-isobutyryloxythymol (6), and 8-hydroxy-9,10-diisobutyryloxythymol (7), were isolated from Centipeda minima. Their structures were identified by means of spectroscopic analyses. Interestingly, compound 2 is not an extraction artifact according to a close HPLC examination of material after extraction by analytical MeOH at ambient temperature. The antibacterial activities of compounds 1-7 were evaluated against eight microbial strains by the agar dilution method.     

Using fractal to solve the multiple minima problem in molecular mechanics calculation

This article presents an approach using fractal to solve the multiple minima problem. We use the Newton–Raphson method of the MM3 molecular mechanics program to scan the conformational spaces of a model molecule and a real molecule. The results show each energy minimum, maximum point, and saddle point has a basin of initial points converging to it in conformational spaces. Points converging to different extrema are mixed, and form fractal structures around basin boundaries. Singular points seem to involve in the formation of fractal. When searching within a small region of fractal basin boundaries, the self‐similarity of fractal makes it possible to find all energy minima, maxima, and saddle points from which global minimum may be extracted. Compared with other methods, this approach is efficient, accurate, conceptually simple, and easy to implement. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1101–1108, 2000     

A Comparison of radiationless transitions involving single-minimum and double minima potential energy surfaces

The quantum-statistical-mechanical (QSM) approach to molecular relaxation phenomena is employed to compare radiationless transitions originating from an electronic state characterized by a single minimum and double minima potential surface for a vibronically active, non-totally symmetric mode. The vibronic level dependence of the decay rates of these two cases has been investigated for both small and large energy gap transitions. It is shown that the behavior of a molecular system is quite different for an initial state possesing a double minima potential surface as compared to the case in which the initial state possesses a single minimum.     

Free energy landscape for glucose condensation reactions

Ab initio molecular dynamics and metadynamics simulations were used to determine the free energy surfaces (FES) for the acid catalyzed β-D-glucose condensation reaction. Protonation of C1-OH on the β-D-glucose, breakage of the C1-O1 bond, and the formation of C1 carbocation is the rate-limiting step. The effects of solvent on the reaction were investigated by determining the FES both in the absence and presence of solvent water. It was found that water played a critical role in these reactions. The reaction barrier for the proton-catalyzed glucose condensation reaction is solvent induced because of proton's high affinity for water. During these simulations, β-D-glucose conversion to α-d-glucose process via the C1 carbocation was also observed. The associated free energy change and activation barrier for this reaction were determined.     

Protein structure and dynamics from single-molecule fluorescence resonance energy transfer

The pros and cons of single-molecule vs ensemble-averaged fluorescence resonance energy transfer (FRET) experiments, performed on proteins, are explored with the help of Langevin dynamics simulations. An off-lattice model of the polypeptide chain is employed, which gives rise to a well-defined native state and two-state folding kinetics. A detailed analysis of the distribution of the donor-acceptor distance is presented at different points along the denaturation curve, along with its dependence on the averaging time window. We show that unique information on the correlation between structure and dynamics, which can only be obtained from single-molecule experiments, is contained in the correlation between the donor-acceptor distance and its displacement. The latter is shown to provide useful information on the free energy landscape of the protein, which is complementary to that obtained from the distribution of donor-acceptor distances.     

MolE8: finding DFT potential energy surface minima values from force-field optimised organic molecules with new machine learning representations

The use of machine learning techniques in computational chemistry has gained significant momentum since large molecular databases are now readily available. Predictions of molecular properties using machine learning have advantages over the traditional quantum mechanics calculations because they can be cheaper computationally without losing the accuracy. We present a new extrapolatable and explainable molecular representation based on bonds, angles and dihedrals that can be used to train machine learning models. The trained models can accurately predict the electronic energy and the free energy of small organic molecules with atom types C, H N and O, with a mean absolute error of 1.2 kcal mol⁻¹. The models can be extrapolated to larger organic molecules with an average error of less than 3.7 kcal mol⁻¹ for 10 or fewer heavy atoms, which represent a chemical space two orders of magnitude larger. The rapid energy predictions of multiple molecules, up to 7 times faster than previous ML models of similar accuracy, has been achieved by sampling geometries around the potential energy surface minima. Therefore, the input geometries do not have to be located precisely on the minima and we show that accurate density functional theory energy predictions can be made from force-field optimised geometries with a mean absolute error 2.5 kcal mol⁻¹.

New representations and machine learning calculate DFT minima from force field geometries.     

A potential energy surface survey of OB6: global minima and isomerization stability

In light of the very recent significant discrepancies on the global isomer of the sept-atomic molecule OB₆, we performed a detailed potential energy surface survey of OB₆ covering various isomeric forms. We showed that at the CCSD(T)/6-311+G(2df)//B3LYP/6-311+G(d) level, the planar knife-like isomer 01 with a –BO moiety has the lowest energy, followed by the planar belt-like isomer 02 at 22.6 kcal/mol. Another isomer 05 at 33.1 kcal/mol can be viewed as the direct O-adduct of the pentagonal pyramid B₆. Kinetically, the three isomers 01, 02 and 05 all have considerable barriers (19–29 kcal/mol) (obtained at B3LYP/6-311+G(d) level) against isomerization. However, other isomers either have much higher energy or possess much smaller conversion barriers and are thus of little likeliness for isolation. Moreover, though being isoelectronic to the well-known CB ₆ ^2? molecule, OB₆ does not have any kinetically stabilized wheel-like isomers with O or B centers. The three OB₆ isomers 01, 02 and 05 await future laboratory studies. The detailed results reported in this paper are expected to provide useful information for understanding the growing process of boron oxides, O-doping and oxidation mechanism of boron clusters.     

The energy landscape of a selective tumor-homing pentapeptide

Recently, a potentially powerful strategy based on phage-display libraries has been presented to target tumors via homing peptides attached to nanoparticles. The Cys-Arg-Glu-Lys-Ala (CREKA) peptide sequence has been identified as a tumor-homing peptide that binds to clotted plasmas proteins present in tumor vessels and interstitium. The aim of this work consists of mapping the conformational profile of CREKA to identify the bioactive conformation. For this purpose, a conformational search procedure based on modified simulated annealing combined with molecular dynamics was applied to three systems that mimic the experimentally used conditions: (i) the free peptide; (ii) the peptide attached to a nanoparticle; and (iii) the peptide inserted in a phage display protein. In addition, the free peptide was simulated in an ionized aqueous solution environment, which mimics the ionic strength of the physiological medium. Accessible minima of all simulated systems reveal a multiple interaction pattern involving the ionized side chains of Arg, Glu, and Lys, which induces a beta-turn motif in the backbone observed in all simulated CREKA systems.     

Calculations of the energy distribution from perturbation peak data--a new tool for characterization of chromatographic phases

The calculation of the adsorption energy distribution (AED) was recently introduced as an important tool for the chromatographic community for characterization of modern phases. The AED-calculations, provides model-independent information about the numbers of different adsorption sites and their respective energy-levels, prior to the selection of an adsorption isotherm model which narrows the number of possible rival models. The selection of a proper model for the fitting of the determined raw data is crucial; if the wrong model is selected misleading information about the retention mechanism may be drawn. The AED-calculations require raw adsorption isotherm data (i.e. data points) which is unfortunately not obtained by the newly validated perturbation peak method. In this study, we developed mathematical expression allowing the use of the raw tangential slope provided by the perturbation peak method for AED calculations. The approach worked excellently and was verified against both computer-generated adsorption isotherm data as well as experimentally determined data, using three different experimental systems. It was found that the calculations of the AED, as based on perturbation peak data, converts faster and are not more sensitive to experimental noise as compared to the classical AED calculations using raw adsorption isotherm data.     

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

There is considerable interest in developing methodologies for the accurate evaluation of free energies, especially in the context of biomolecular simulations. Here, we report on a reexamination of the recently developed metadynamics method, which is explicitly designed to probe "rare events" and areas of phase space that are typically difficult to access with a molecular dynamics simulation. Specifically, we show that the accuracy of the free energy landscape calculated with the metadynamics method may be considerably improved when combined with umbrella sampling techniques. As test cases, we have studied the folding free energy landscape of two prototypical peptides: Ace-(Gly)(2)-Pro-(Gly)(3)-Nme in vacuo and trialanine solvated by both implicit and explicit water. The method has been implemented in the classical biomolecular code AMBER and is to be distributed in the next scheduled release of the code.     

Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening

Although virtual screening through molecular docking has been widely applied in lead discovery, it is still challenging to distinguish true hits from high-scoring decoys because of the difficulty in accurately predicting protein-ligand binding affinities. Following the successful application of energy landscape analysis to both protein folding and biomolecular binding studies, we attempted to use protein-ligand binding energy landscape analysis to recognize true binders from high-scoring decoys. Two parameters describing the binding energy landscape were used for this purpose. The energy gap, defined as the difference between the binding energy of the native binding mode and the average binding energy of other binding modes in the "denatured binding phase", was used to describe the thermodynamic stability of binding, and the number of local binding wells in the landscapes was used to account for the kinetic accessibility. These parameters, together with the docking score, were combined using logistic regression to investigate their capability to discriminate true ligands from high-scoring decoys. Inhibitors and the noninhibitors of two enzyme systems, neuraminidase and cyclooxygenase-2, were used to test their discrimination capability. Using a five-fold cross-validation, the areas under the receiver operator characteristic curves (AUCs) from the best linear combinations of parameters reached 0.878 for neuraminidase and 0.776 for cyclooxygenase-2. To make a more independent test, inhibitors and high-scoring decoys in a directory of useful decoys (DUD), the largest and most comprehensive public data set for benchmarking virtual screen programs by far, were used as independent test sets to test the discrimination capability of these parameters. The AUCs of the best linear combinations of parameters for the independent test sets were 0.750 for neuraminidase and 0.855 for cyclooxygenase-2. Furthermore, combining these two parameters with the docking scoring function improved the enrichment ratio to 200-300% compared to that using the scoring function alone. This study suggests that incorporating information from binding energy landscape analysis can significantly increase the success rate of virtual screening.     

Feasibility of peak volume,side pixel and multiple peak registration in high-resolution continuum source atomic absorption spectrometry

In high-resolution continuum source atomic absorption spectrometry (HR-CS AAS) with a pixel detector, such as a charge-coupled device array for signal registration, the absorbance A not only depends on the absorption coefficient, the length of the absorbing layer and the number of absorbing atoms therein, but also on the spectral interval over which the signal is recorded, i.e., the spectral bandwidth per pixel and the number of pixels evaluated. Although the problem of different (absorption and emission) line widths is known for several decades already to exist in conventional line source AAS, it is usually disregarded. By choosing a certain number of pixels in HR-CS AAS a defined wavelength interval can be selected over which the absorbance is recorded. As the numerical values obtained this way are not directly comparable with the conventional absorbance, it is necessary to define new terms and symbols for this kind of signal evaluation. With a steady-state signal the individual pixel absorbance values can be added or integrated, resulting in the unit-free wavelength-selected absorbance (WSA, symbol A_Σ), or the wavelength-integrated absorbance (WIA, symbol A_λ) having a wavelength unit, such as picometers (pm). Similarly, with transient signals one can add-up or integrate (over wavelength) the individual integrated (in time) absorbance values of the selected pixels to obtain the volume under the absorbance peak. This results in the peak volume selected absorbance (PVSA, symbol A_Σ,int), and the peak volume integrated absorbance (PVIA, symbol A_λ,int), with the units second (s) and second times picometer (s pm), respectively. For comparison purposes, however, the integrated absorbance values, i.e., WIA or PVIA, should be used since they are instrument-independent.     

Potential energy landscape of bis(fluorosulfonyl)amide

The conformational landscape of the bis(fluorosulfonyl)amide, [FSI]-, anion was analyzed using data obtained from Raman spectroscopy, molecular dynamics (MD), and ab initio studies. The plotting of three-dimensional potential energy surfaces and the corresponding MD simulation conformer-population histograms show the existence of two stable isomers, C2 (trans) and C1 (cis) conformers, and confirm the nature of the anion as a flexible molecule capable of interconversion between conformers in the liquid state. In ionic liquids, the two [FSI]- conformers coexist in equilibrium, a result confirmed by the Raman data. The implications of the conformational behavior of the ion [FSI]- are discussed in terms of the solvation properties of the corresponding ionic liquids.