Potential Energy Calculations Research Articles

New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures.

Accurate prediction of a protein's structure requires a reliable free energy function that consists of both enthalpic and entropic contributions. Although considerable progresses have been made in the calculation of potential energies in protein structure prediction, the computation for entropies of protein has lagged far behind, due to the challenge that estimation of entropies often requires expensive conformational sampling. In this study, we have used a knowledge-based approach to estimate the backbone conformational entropies from experimentally determined structures. Instead of conducting computationally expensive MD/MC simulations, we obtained the entropies of protein structures based on the normalized probability distributions of back dihedral angles observed in the native structures. Our new knowledge-based scoring function with inclusion of the backbone entropies, which is referred to as ITScoreDA or ITDA, was extensively evaluated on 16 commonly used decoy sets and compared with 50 other published scoring functions. It was shown that ITDA is significantly superior to the other tested scoring functions in selecting native structures from decoys. The present study suggests the role of backbone conformational entropies in protein structures and provides a way for fast estimation of the entropic effect.

Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

Improved continuum lowering calculations in screened hydrogenic model with l-splitting for high energy density systems

The energy states of the bound electrons in high energy density systems (HEDS) are significantly affected due to the electric field of the neighboring ions. Due to this effect bound electrons require less energy to get themselves free and move into the continuum. This phenomenon of reduction in potential is termed as ionization potential depression (IPD) or the continuum lowering (CL). The foremost parameter to depict this change is the average charge state, therefore accurate modeling for CL is imperative in modeling atomic data for computation of radiative and thermodynamic properties of HEDS. In this paper, we present an improved model of CL in the screened hydrogenic model with l-splitting (SHML) proposed by G. Faussurier and C. Blancard, P. Renaudin [High Energy Density Physics 4 (2008) 114] and its effect on average charge state. We propose the level charge dependent calculation of CL potential energy and inclusion of exchange and correlation energy in SHML. By doing this, we made our model more relevant to HEDS and free from CL empirical parameter to the plasma environment. We have implemented both original and modified model of SHML in our code named OPASH and benchmark our results with experiments and other state-of-the-art simulation codes. We compared our results of average charge state for Carbon, Beryllium, Aluminum, Iron and Germanium against published literature and found a very reasonable agreement between them.

Study on potential tsunami by earthquake in subduction zone of Sulawesi Sea

Indonesia is one country in the world featuring a complex tectonic structure. This condition makes earthquakes often occur in many areas of this country and as an earthquake rages beneath the sea, it will potentially trigger tsunami. One of the areas in Indonesia with a high seismic activity is Sulawesi region particularly in the Sulawesi Sea subduction zone, making it important to carry out a study on the potential tsunami at this location. The purpose of this study was to analyze the existing huge potential energy in Sulawesi Sea subduction zone and to identify tsunami modeling likely to occur based on the potential energy of the region. The approach used in assessing the tsunami disaster was the calculation of the potential energy of an earthquake and tsunami modeling based on the potential energy. The method used in this research was the least squares method for the calculation of potential energy, and near-field tsunami modeling with the assistance of TUNAMI-N2 COD. The research finding has shown that the Sulawesi Sea subduction zone has potential energy of 1.35469 × 1023 erg, equivalent to an earthquake with a magnitude of 7.6 Mw. The tsunami modeling made shown the average wave propagation reaching ashore within 12.3 min with a height varying between 0.1 and > 3 m. The tsunami modeling also indicated that there are seven sub-districts in Buol District, Central Sulawesi, which is affected by a significant tsunami.

One- and two-phonon γ -vibrational bands in neutron-rich Mo107

Neutron-rich $^{107}\mathrm{Mo}$ has been reinvestigated by analyzing the large statistics $\ensuremath{\gamma}\ensuremath{-}\ensuremath{\gamma}\ensuremath{-}\ensuremath{\gamma}$ and $\ensuremath{\gamma}\ensuremath{-}\ensuremath{\gamma}\ensuremath{-}\ensuremath{\gamma}\ensuremath{-}\ensuremath{\gamma}$ coincidence data from the spontaneous fission of $^{252}\mathrm{Cf}$ at the Gammasphere detector array. Two new bands have been identified. The potential-energy surface calculations of this nucleus have been performed. The calculations show evidence for the $5/{2}^{+}[413]$ configuration of the ground-state band and $7/{2}^{\ensuremath{-}}[523]$ configuration for the 348-keV excited band, as assigned in previous work. The two bands newly established are proposed to be one- and two-phonon $\ensuremath{\gamma}$-vibrational bands built on the $7/{2}^{\ensuremath{-}}[523]$ Nilsson orbital, respectively, in the current paper. Triaxial projected shell-model (TPSM) calculations have been performed to explain the level structure and are found in fair agreement with experimental data. In particular, the TPSM study confirms the $\ensuremath{\gamma}$- and $\ensuremath{\gamma}\ensuremath{\gamma}$-vibrational structure for the two observed excited band structures. Systematics of the one- and two-phonon $\ensuremath{\gamma}$-vibrational bands in the $A\ensuremath{\sim}100$ Mo series is also discussed.

Synthesis, structure, and phase transition of a novel proton transfer in a supramolecular cation with 2-nitroanilinium based on 18-crown-6

One novel inorganic–organic hybrid supramolecular compound named (2-nitroanilinium)(18-crown-6)(IO4) (1) has been synthesized and characterized through single-crystal X-ray diffraction, elemental analysis, infrared analysis, thermogravimetric analysis, differential scanning calorimetry (DSC), and potential energy calculations. DSC measurements show a pair of reversible peaks at 260.5 (cooling) and 264.5 K (heating) with heat hysteresis of approximately 4 K. These characteristics indicate that this supramolecular compound undergoes a reversible phase transition, as confirmed by temperature-dependent dielectric measurements. Structural analysis and potential energy calculations demonstrate that dielectric anomaly and phase transition occur because of the intramolecular and intermolecular proton transfer of NH3+ in 2-nitroanilinium as a consequence of NO2 motion in the cation.

Correlating Properties in Iron(III) Complexes: A DFT Description of Structure, Redox Potential and Spin Crossover Phenomena

Calculations of structure, redox potential and spin transition energies were performed using DFT approximations for a series of [Fe(bztpen)OR]2+/+ type FeIII/FeII systems (R=Me, Et, nPr, nBu), which have a temperature dependent spin crossover behavior. These compounds exhibit changes in redox and magnetic properties, related to structural variations quite important for their possible applications among which signal generator materials stand out. Functionals B3LYP, ωB97X−D and TPSS along with PCM solvation model were evaluated for redox potential, whereas for spin crossover the TPSSh functional was also included. The multireference character of these compounds was tested as well. Calculations were compared to experimental measurements, and ωB97X−D proved able to accurately describe the geometries observed in solid state for the low spin (LS) and high spin (HS) states; moreover, it had the best correlation between calculated and experimental redox potential values. However, in the description of the spin transition energies the TPSS functional is needed to correctly describe the LS state as the observed ground state in the complexes at low temperature, which allows to calculate proper spin transition curves as a function of temperature. From these results, we obtained suitable approximations for an accurate description of redox potential and magnetic properties for the FeIII coordination compounds, which can be extended to model similar systems.

On the mechanism of non-radiative decay of blue fluorescent protein chromophore: New insight from the excited-state molecular dynamics simulations and potential energy calculations

A detailed theoretical investigation based on the ab initio on-the-fly surface hopping dynamics simulations and potential energy surfaces calculations has been performed to unveil the mechanism of the photoinduced non-adiabatic relaxation process of the isolated blue fluorescent protein (BFP) chromophore in gas phase. The data analysis presents that the dominant reaction coordinate of the BFP chromophore is driven by a rotation motion around the CC double bridging bond, which is in remarkable difference with a previous result which supports a Hula-Twist rotation pattern. Such behavior is consistent with the double bond rotation pattern of the GFP neutral chromophore. In addition, the dynamics simulations give an estimated decay time of 1.1ps for the S1 state, which is agrees well with the experimental values measured in proteins. The present work offers a straightforward understanding for the decay mechanism of the BFP chromophore and suggestions of the photochemical properties of analogous protein chromophores. We hope the current work would be helpful for further exploration of the BFP photochemical and photophysical properties in various environments, and can provide guidance and prediction for rational design of the fluorescent proteins catering for different demands.

Cs/CsPbX3 (X = Br, Cl) epitaxial heteronanocrystals with magic-angle stable/metastable grain boundary

Metal-semiconductor heteronanostructures are crucial building blocks of nanoscale electronic and optoelectronic devices. However, the lattice misfit remains a challenge in constructing heteronanostructures. Perovskite nanocrystals are superior candidates for constructing nanodevices owing to excellent optical, ferroelectric, and superconducting properties. We report the epitaxial growth of lattice-matched Cs/CsPbBr3 metal-semiconductor heteronanocrystals in a liquid medium. The well-crystallized ultrathin Cs layers grow epitaxially on the surfaces of colloidal CsPbBr3 nanocrystals, forming heteronanocrystals with interface diameters of several nanometers. Most of them are pseudomorphic with coherent interfaces free from dislocations, and the others exhibit discrete high-angle grain boundaries. The model based on the calculation of the elastic potential energy of the epilayer and analysis of the near-coincidence sites explains well the experimental result. The analysis shows that the excellent lattice match between the metal and the semiconductor ensures the ideal epitaxial-growth of both Cs/CsPbBr3 and Cs/CsPbCl3 heteronanocrystals. Such metal/semiconductor heteronanocrystals pave the way for developing perovskite-based nanodevices.

Analiz potentsial'noyi enerhiyi systemy vzayemodiyuchykh chastynok, uporyadkovanykh u gratku Brave

We propose a method to calculate the type of a lattice formed by grains in dusty plasma and estimate its potential energy. Basically, this task is complicated by the interparticle potential that appertains to “catastrophic potentials”. This kind of potentials needs special approaches to avoid divergences during potential energy calculations. In the current contribution, we will develop all the necessary modifications to appropriate methods. It will be shown that the obtained potential energy expression can be used to determine lattice parameters and these parameters comply to known experimental data.

Are fluorine-based contacts predictable? A case study in three similar coordination compounds

The crystal structures of three similar Hg(II) complexes including the N-(2,5-difluorophenyl)-2-pyrazinecarboxamide ligand were determined by X-ray diffraction. In each structure, the fluorine atoms were involved in different, non-predictable fluorine-based contacts. Quantitative analysis of the potential surface and interaction energy calculations were performed for the different interactions involving fluorine.

Effect of Methylation on the Photodynamical Behavior of Arylazoimidazoles: New Insight from Theoretical ab Initio Potential Energy Calculations and Molecular Dynamics Simulations.

Arylazoimidazoles are a series of azobenzene derivatives possessing the ability to undergo photoinduced trans-cis isomerization. Their isomerization quantum yields are found to be dependent on the excitation wavelength and chemical substituents. The current work investigated the ultrafast nonadiabatic decay behaviors of three arylazoimidazoles (Pai-H, Tai-H, and Tai-Me) after being photoexcited to the S1 and S2 states by means of high-level ab initio potential energy calculations and on-the-fly surface hopping dynamical simulations in gas phase to explore the effect of the methylation. The results found that the Pai-H with no methylation substituents only decay along a NNC bending reaction pathway for both the S1 and S2 states. The Tai-H with a methylation substituent on the six-membered ring can decay along both the NNC bending and twisting motion pathways for the S1 and S2 states. The Tai-Me has methylation substituents on both the six- and five-membered rings prefers to decay by a twisting motion in the S1 state, while a NNC bending channel is activated following excitation to the S2 state. The position and numbers of methylation substituents has important influence on the dynamical behaviors of arylazoimidazoles. The current work provides fundamental knowledge of the arylazoimidazoles and will be helpful for advanced and further exploration and application.

CaH Rydberg series, oscillator strengths and photoionization cross sections from Molecular Quantum Defect and Dyson Orbital theories

In this work, electron-propagator methods are applied to the calculation of the ionization potential and vertical excitation energies for several Rydberg series of the CaH molecule. The present calculations cover more highly excited states than those previously reported. In particular, excitation energies for ns (n>5), np (n>5), nd (n>4) and nf Rydberg states are given. Oscillator strengths for electronic transitions involving Rydberg states of CaH, as well as photoionization cross sections for Rydberg channels, also have been determined by using the Molecular Quantum Defect Orbital approach. Good agreement has been found with the scarce comparative data that are available for oscillator strengths. To our knowledge, predictions of photoionization cross sections from the outermost orbital of CaH are made here for the first time. A Cooper minimum and mixed atomic orbital character in some of the Dyson orbitals are among the novel features of these present calculations.

Synthesis, characterization, and phase transition of an inorganic–organic hybrid compound, [(3-nitroanilinium+)(18-crown-6)][IO4−](CH3OH)

A novel inorganic–organic hybrid supramolecular compound, [(3-nitroanilinium+)(18-crown-6)][IO4−](CH3OH) (1), was discovered as phase-transition materials displaying dielectric anomalous behaviors. The yellow block crystal formed by N–H···O hydrogen bonding that made contact through the cavity of 18-crown-6 was characterized by single-crystal X-ray diffraction, elemental analysis, infrared analysis, thermogravimetric analysis, differential scanning calorimetry, and potential-energy calculations. Differential scanning calorimetry measurements indicate that the compound experiences a reversible phase transition at around 220K. Temperature-dependent dielectric measurements further confirm the phase transitions. Potential-energy calculations demonstrate that the phase transition occurs due to the molecular order–disorder rotation of CH3OH, whereas the space grouping of the crystal remains unchanged.

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate.

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D‐UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine 1La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine 1Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter‐base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long‐lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the 1Lb, S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D‐UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm−1 in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D‐UV spectroscopy to disentangle the photophysics of multichromophoric systems.

Pseudospectral Gaussian quantum dynamics: Efficient sampling of potential energy surfaces.

Trajectory-based Gaussian basis sets have been tremendously successful in describing high-dimensional quantum molecular dynamics. In this paper, we introduce a pseudospectral Gaussian-based method that achieves accurate quantum dynamics using efficient, real-space sampling of the time-dependent basis set. As in other Gaussian basis methods, we begin with a basis set expansion using time-dependent Gaussian basis functions guided by classical mechanics. Unlike other Gaussian methods but characteristic of the pseudospectral and collocation methods, the basis set is tested with N Dirac delta functions, where N is the number of basis functions, rather than using the basis function as test functions. As a result, the integration for matrix elements is reduced to function evaluation. Pseudospectral Gaussian dynamics only requires O(N) potential energy calculations, in contrast to O(N(2)) evaluations in a variational calculation. The classical trajectories allow small basis sets to sample high-dimensional potentials. Applications are made to diatomic oscillations in a Morse potential and a generalized version of the Henon-Heiles potential in two, four, and six dimensions. Comparisons are drawn to full analytical evaluation of potential energy integrals (variational) and the bra-ket averaged Taylor (BAT) expansion, an O(N) approximation used in Gaussian-based dynamics. In all cases, the pseudospectral Gaussian method is competitive with full variational calculations that require a global, analytical, and integrable potential energy surface. Additionally, the BAT breaks down when quantum mechanical coherence is particularly strong (i.e., barrier reflection in the Morse oscillator). The ability to obtain variational accuracy using only the potential energy at discrete points makes the pseudospectral Gaussian method a promising avenue for on-the-fly dynamics, where electronic structure calculations become computationally significant.

Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation.

Lipoxygenases (LOXs) are a family of enzymes involved in the biosynthesis of several lipid mediators. In the case of human 15-LOX, the 15-LOX-1 and 15-LOX-2 isoforms show slightly different reaction regiospecificity and substrate specificity, indicating that substrate binding and recognition may be different, a fact that could be related to their different biological role. Here, we have used long molecular dynamics simulations, QM(DFT)/MM potential energy and free energy calculations (using the newly developed DHAM method), to investigate the binding mode of the arachidonic acid (AA) substrate into 15-LOX-2 and the rate-limiting hydrogen-abstraction reaction 15-LOX-2 catalyzes. Our results strongly indicate that hydrogen abstraction from C13 in 15-LOX-2 is only consistent with the "tail-first" orientation of AA, with its carboxylate group interacting with Arg429, and that only the pro-S H13 hydrogen will be abstracted (being the pro-R H13 and H10 too far from the acceptor oxygen atom). At the B3LYP/6-31G(d) level the potential and free energy barriers for the pro-S H13 abstraction of AA by 15-LOX-2 are 18.0 and 18.6 kcal/mol, respectively. To analyze the kinetics of the hydrogen abstraction process, we determined a Markov model corresponding to the unbiased simulations along the state-discretized reaction coordinate. The calculated rates based on the second largest eigenvalue of the Markov matrices agree well with experimental measurements, and also provide the means to directly determine the pre-exponential factor for the reaction by comparing with the free energy barrier height. Our calculated pre-exponential factor is close to the value of kBT/h. On the other hand, our results suggest that the spin inversion of the complete system (including the O2 molecule) that is required to happen at some point along the full process to lead to the final hydroperoxide product, is likely to take place during the hydrogen transfer, which is a proton coupled electron transfer. Overall, a different binding mode from the one accepted for 15-LOX-1 is proposed, which provides a molecular basis for 15-LOX-2 exclusive 15-HPETE production in front of the double (although highly 15-) 12/15 regiospecificity of 15-LOX-1. Understanding how these different isoenzymes achieve their regiospecificity is expected to help in specific inhibitor design.

Identification of overlapping resonances in dissociative electron attachment to chlorine molecules

A combined highly differential momentum imaging experiment and ab initio potential-energy curve calculation using density-functional theory (DFT) have been performed to understand the broad resonant peak around 5.7 eV due to dissociative electron attachment (DEA) to the chlorine molecule. Both the kinetic energy and angular distribution over the entire $2\ensuremath{\pi}$ angle of the fragment negative ions have been measured. Two heavily overlapping resonances are identified for the observed broad resonant peak that could settle the long-standing debate. The symmetry of the involved two temporary negative ion (TNI) states are determined from the angular distribution data. Experimental observations are strongly supported with the computed potential-energy curve using DFT.

Calculation of Potential Energy Concerning "H + Cl2 → HCl + Cl" and Production of CG Movie for Learner to Acquire Its Image with Structures of Reactants and Reaction Profile

Calculation of Potential Energy Concerning "H + Cl₂ → HCl + Cl" and Production of CG Movie for Learner to Acquire Its Image with Structures of Reactants and Reaction Profile

Structures and thermal properties of the N2 monolayer on Pb(1 1 1)

The physisorption of N2 molecules has long been a model system of molecular adsorption. We present a low-energy electron diffraction (LEED) study of the adsorption structures and thermodynamics of monolayer N2 on Pb(1 1 1). The results indicate that the monolayer structure has a triangular incommensurate center-of-mass lattice, and that the N2-substrate interaction is weaker than that observed on other metal surfaces. The N2 monolayer undergoes a phase transition between an orientationally ordered phase (low-temperature) and an orientationally disordered phase at a temperature of 20 K. Potential energy and quasiharmonic calculations indicate that the weak N2-Pb(1 1 1) interaction is the main contributing factor for the difference in orientational order of incommensurate N2 monolayers on Pb(1 1 1) and other similar metal surfaces.