Ab Initio Born-Oppenheimer Molecular Dynamics Research Articles

Achieving High Substitutional Incorporation in Mn-Doped Graphene.

Despite its broad potential applications, substitution of carbon by transition metal atoms in graphene has so far been explored only to a limited extent. We report the realization of substitutional Mn doping of graphene to a record high atomic concentration of 0.5%, which was achieved using ultralow-energy ion implantation. By correlating the experimental data with the results of ab initio Born-Oppenheimer molecular dynamics calculations, we infer that direct substitution is the dominant mechanism of impurity incorporation. Thermal annealing in ultrahigh vacuum provides efficient removal of surface contaminants and additional implantation-induced disorder, resulting in Mn-doped graphene that, aside from the substitutional Mn impurities, is essentially as clean and defect-free as the as-grown layer. We further show that the Dirac character of graphene is preserved upon substitutional Mn doping, even in this high concentration regime, making this system ideal for studying the interaction between Dirac conduction electrons and localized magnetic moments. More generally, these results show that ultralow energy ion implantation can be used for controlled functionalization of graphene with substitutional transition-metal atoms, of relevance for a wide range of applications, from magnetism and spintronics to single-atom catalysis.

Methanediol CH2(OH)2 and hydroxymethyl CH2OH+: key organic intermediates on the path to complex organic molecules

Context. Ab initio molecular dynamics simulations were carried out to study the formation pathways to complex organic molecules when a OH+ projectile hit an interstellar dust grain covered only by methanol molecules. The selected target material is a methanol cluster formed by ten units (CH3OH)10. Aims. The focus of this paper is the process where methanediol CH2(OH)2 and hydroxymethyl CH2OH+, both key organic intermediate molecules, were involved in the formation mechanisms of stable complex organic molecules (COMs). Methods. We performed Born-Oppenheimer (ab initio) molecular dynamics (BOMD) simulations under the hybrid functional of Head-Gordon ωB97X-D. We used the initial kinetic impact energy of 10, 12, 15, 18, 20, and 22 eV. Results. We corroborate that CH2(OH)2 and CH2OH+ are the main precursors to form molecules such as methoxymethanol CH3OCH2OH, the formyl radical HCO, the Criegee biradical CH2OO, and formaldehyde H2Co and its elusive HCOH isomer. We discuss the mechanism formation of these complex organic molecules. We compare the formation pathways with previous theoretical results where both key intermediates are present. The pathways in some cases go through CH2(OH)2 or undergo by CH2OH+. Conclusions. We confirm that CH2(OH)2 and CH2OH+ play a key role on the path to the formation of abundant H2CO. These mechanisms can give insight into alternative pathways relevant to understanding experimental processes with key steps within those precursors.

Benchmarking Plane Waves Quantum Mechanical Calculations of Iron(II) Tris(2,2′-bipyridine) Complex by X-ray Absorption Spectroscopy

In this work, we used, for the first time, a computational Self-Consistent Field procedure based on plane waves to describe the low and high spin conformational states of the complex [Fe(bpy)3]2+. The results obtained in the study of the minimum energy structures of this complex, a prototype of a wide class of compounds called Spin Cross Over, show how the plane wave calculations are in line with the most recent studies based on gaussian basis set functions and, above all, reproduce within acceptable errors the experimental spectra of X-ray absorption near-edge structure spectroscopy (XANES). This preliminary study shows the capabilities of plane wave methods to correctly describe the molecular structures of metal-organic complexes of this type and paves the way for future even complex computational simulations based on the energy gradient, such as Nudge Elastic Band or ab-initio Born-Oppenheimer molecular dynamics.

Electrochemical oxygen reduction reaction at conductive polymer PEDOT: Insight from ab initio molecular dynamics simulations

Conducting polymers such as poly (3,4-ethylenedioxythiophene) (PEDOT) have attracted research attention as promising effective electrocatalytic materials for Oxygen Reduction Reaction (ORR). However, the complete reaction pathways leading to the hydrogen peroxide, H2O2, formation still remained unexplored. In this study, ab initio Born–Oppenheimer molecular dynamics (MD) calculations with an explicit solvent, were carried out to investigate the detailed mechanisms of the ORR on PEDOT via monitoring MD trajectories and analysing electronic energies. We confirm the outer-sphere nature of the first electron transfer and describe the essentially concerted electron–proton transfer nature of both oxygen reduction steps. Proton transfer is found to be involved in the first and second reduction steps and the role of water as an explicit solvent is outlined. Formation of the hydrogen peroxide is observed via either the reduction of hydroperoxyl radical HO2 or cleavage of its peroxo-adduct with PEDOT. It is therefore theoretically validated that the O2 reduction on a PEDOT may proceed a series pathway occurring simultaneously in acidic media. This approach provides an efficient and reliable means to rationalize and predict reaction mechanisms in solvent environment.

Investigating Primary Charge Separation in the Reaction Center of Heliobacterium modesticaldum.

We compute the primary charge separation step in the homodimeric reaction center (RC) of Heliobacterium modesticaldum from first principles. Using time-dependent density functional theory with the optimally tuned range-separated hybrid functional ωPBE, we calculate the excitations of a system comprising the special pair, the adjacent accessory bacteriochlorophylls, and the most relevant parts of the surrounding protein environment. The structure of the excitation spectrum can be rationalized from coupling of the individual bacteriochlorophyll pigments similar to molecular J- and H-aggregates. We find excited states corresponding to forward-charge transfer along the individual branches of the RC of H. modesticaldum. In the spectrum, these are located at an energy between the coupled Qy and Qx transitions. With ab initio Born-Oppenheimer molecular dynamics simulations, we reveal the influence of thermal vibrations on the excited states. The results show that the energy gap between the coupled Qy and the forward-charge transfer excitations is ∼0.4 eV, which we consider to conflict with the concept of a direct transfer mechanism. Our calculations, however, reveal a certain spectral overlap of the forward-charge transfer and the coupled Qx excitations. The reliability and robustness of the results are demonstrated by several numerical tests.

Born-Oppenheimer molecular dynamics simulations on structures of high-density and low-density water: a comparison of the SCAN meta-GGA and PBE GGA functionals.

Using Born-Oppenheimer ab initio molecular dynamics (BOAIMD) simulations, the high-density water (HDW) and low-density water (LDW) structures based on SCAN meta-GGA are compared with those based on PBE GGA. Compared with Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations, BOAIMD simulations can produce more accurate results because no fictitious electron mass is introduced. At each state point, our simulations continue for 100 ps after the system reached equilibrium, which is the longest ab initio simulations of liquid water reported so far and can ensure an accurate statistical average. The influence of the size effect and nuclear quantum effect on structure is not considered in the present work, but only that of two different functionals on the structure is discussed. It is found that, in HDW, just as shown using CPAIMD simulations, the SCAN-based hydrogen-bonds (HBs) are more flexible than the PBE-based ones, which makes the structure based on SCAN obviously closer to the experimental results than that based on PBE. However, it is not the case in LDW, and the difference between the results based on these two functionals is very small.

PyHMA: A VASP post-processor for precise measurement of crystalline anharmonic properties using harmonically mapped averaging

We introduce a new Python package (pyHMA) that interfaces with VASP to compute (classical) anharmonic properties of crystalline systems by post-processing data from NVT Born–Oppenheimer ab initio molecular dynamics (AIMD) simulation. It is based on the recently developed harmonically mapped averaging (HMA) method, which leverages the analytically known harmonic behavior to reformulate the direct/conventional ensemble averages in order to significantly improve precision, for a given CPU time. The package consists of two stages: reading AIMD data from vasprun.xml file(s) and then computing anharmonic properties. While the first stage is MD package-dependent, the second one is universal, given that it receives data in the required format. To demonstrate the usage of pyHMA, we compute anharmonic energy and pressure of aluminum fcc crystal at high pressure (≈115GPa) and up to 4000 K (near melting). We further compute anharmonic free energy as a function of temperature, using thermodynamic integration of the HMA anharmonic energy. Although pyHMA currently interfaces with VASP to compute HMA anharmonic energy and pressure, it is moduled in such a way to allow for interfacing with other codes (e.g., LAMMPS) by adding a new reader and can compute other HMA anharmonic properties (e.g., heat capacity) by adding a new method, once relevant data are available. Program summaryProgram title: pyHMACPC Library link to program files:http://dx.doi.org/10.17632/bzgfk52msk.1Licensing provisions: MPL-2.0Programming language: Python 3.7Nature of problem: Theormodynamic properties (e.g., energy, pressure, and heat capacity) of crystalline systems can be decomposed into: lattice (or, property at 0 K), quasiharmonic, and anharmonic contributions. Although the first two are feasible to compute using only a few single-point density functional theory (DFT) calculations, measuring anharmonic contribution requires running ab initio molecular dynamics (AIMD) simulation, which is computationally very demanding using direct ensemble averaging.Solution method: In pyHMA, we are adopting the harmonically mapped averaging (HMA) technique that provides order(s) of magnitude higher precision, in comparison to direct/conventional (Conv) averaging. The package works as a post-processor to VASP AIMD output to provide very precise (and accurate) estimate of anharmonic properties, for a given DFT model, with application to energy and pressure (at this time).Additional comments: The term anharmonicity is commonly used in literature to qualitatively describe a system with no equilibrium configuration at 0 K (i.e., imaginary frequencies); in other words, it refers to a “non-harmonic” potential-energy surface. Here, however, we define anharmonic contribution of some property X as the residual in excess of the harmonic approximation; Xah≡X−(Xlat+Xqh). Therefore, this specific definition is meaningless if the system does not have equilibrium lattice configuration at 0 K. For this reason, pyHMA checks forces on the first configuration to make sure the system has an equilibrium configuration (i.e., zero forces). In addition, when using pyHMA to measure anharmonic free energy using thermodynamic integration from 0 K (Sec. 3.3), only ground-state DFT must be used; using finite-temperature DFT (i.e., Fermi–Dirac smearing; ISMEAR=-1 and SIGMA=kBT), as often done with metals, cannot be used as the PES in this case is temperature-dependent, which is not accounted for in the integration. This contribution, however, can still be included using free-energy perturbation methods as described elsewhere [1]. On the other hand, for properties that do not require temperature integration (e.g., energy and pressure), pyHMA reads the electronic free-energy surface (F), rather than the ground-state energy (E0); hence, electronic contribution is accounted for.

Dynamics of Water in the Solvation Shell of an Iodate Ion: A Born-Oppenheimer Molecular Dynamics Study.

The iodate ion has an anisotropic structure and charge distribution. It has a pyramidal shape with the iodine atom located at the peak of the pyramid. The water molecules interact differently with the positively charged iodine and the negatively charged oxygen atoms of this anion, giving rise to two distinct solvation shells. In the present study, we have performed ab initio Born-Oppenheimer molecular dynamics simulations to investigate the dynamics of water molecules in the iodine and oxygen solvation shells of the iodate ion and compared the behavior with those of the bulk. The dynamics of water is calculated for both the BLYP and the dispersion-corrected BLYP-D3 functionals at room temperature. The dynamics of water in the solvation shells at higher temperatures of 353 and 330 K has also been investigated for the BLYP and BLYP-D3 functionals, respectively. The hydrogen bond dynamics, vibrational spectral diffusion, orientational and translational diffusion, and residence dynamics of water molecules in the two solvation shells are looked at in the current study. The ion-water hydrogen bond dynamics is found to be somewhat faster than that for water-water hydrogen bonds in the bulk, which can be attributed to a ring-like electron distribution on the iodate oxygens. The dynamical trends are connected to the water structure making/breaking properties of the positively charged iodine and negatively charged oxygen sites of the anion. Furthermore, orientational jumps of the iodate ion and also those of surrounding water molecules which are hydrogen bonded to the oxygen atoms of the iodate ion are also investigated. It is found that the nature of these orientational jumps can be different from those reported earlier for planar polyoxyanions such as the nitrate ion.

Vibrational Predissociation Spectroscopy of Cold Protonated Tryptophan with Different Messenger Tags.

Vibrational spectra of protonated tryptophan were recorded by predissociation of H2 messenger tags using cryogenic ion traps. We explore the issue of messenger induced spectral changes by solvating TrpH+(H2) n with n = 1-5 to obtain single photon vibrational spectra of TrpH+ and of its partly deuterated isotopomer in the spectral region of 800-4400 cm-1. Depending on the number of messenger molecules, the spectra of several conformational isomers associated with multiple H2 binding locations along with two natural conformations of TrpH+ were found using the two photon MS3IR2 conformational hole burning method. Most probable messenger positions were established by comparison with predictions from DFT calculations on various candidate structures. Mechanical anharmonicity effects associated with the charged amino group were modeled by Born-Oppenheimer ab initio molecular dynamics. The spectra of TrpH+(H2O) m=1,2, recorded by infrared multiphoton dissociation (IRMPD), reveal broad features in the NH stretching region of the NH3+ group, indicating strong hydrogen bonding in acceptor-donor configuration with the benzene ring for the first water molecule, while the second water appears to attach to a less strongly perturbing site, yielding unique transitions associated with the free OH stretching fundamentals. We discuss the structural deformations induced by the water molecules and compare our results to recent experiments on similar hydrated cationic systems.

Ab initio molecular dynamics simulation on interfacial reaction behavior of Fe-Cr-Ni stainless steel in high temperature water

The interfacial reaction behavior of Fe-Cr-Ni stainless steel in 320 °C high temperature water is investigated using an ab initio Born-Oppenheimer molecular dynamics simulation. After the Fe-Cr-Ni stainless steel is immersed in water, the water molecule is dissociated into OH and H ions. The dissociated OH makes bond with the Cr and Fe atoms to form (Cr,Fe)-OH hydroxide, and the dissociated H adsorbs on the Fe atoms with a certain negative charge. The surface layers of Fe-Cr-Ni stainless steel are negatively charged before immersion, whereas after immersion there is a net positive charge in the surface layers. Most of the valence electrons lost from the surface layers transfer to the water solution through the interface, only a small amount of electrons comes into the inner layer atoms of Fe-Cr-Ni stainless steel. The dissociation characteristics of dissolved oxygen molecule and dissolved hydrogen molecule in high temperature water are also analyzed, and both of them can enhance the interfacial charge transfer.

Reactivity of the O2+·(H2O)n and NO+·(H2O)n cluster ions in the D-region of the ionosphere.

The protonated water clusters present in the D-region of the ionosphere have been postulated to be formed from cluster ions such as O2+·(H2O)n and NO+·(H2O)n, although the detailed mechanism of the underlying reactions is not understood. Second order Møller-Plesset perturbation theory based Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations of the reactions of the O2+·(H2O)n and NO+·(H2O)n cluster ions to form protonated water clusters reveal different mechanisms for the O2+ and NO+ based ions. AIMD simulations of O2+·(H2O)n=2-5 with initial velocities of the atoms sampled from the Maxwell-Boltzmann distribution at 220 K show that following charge transfer, a reaction to form a protonated water cluster and OH occurs rapidly where the neutral O2 molecule is just a spectator. In contrast, the reaction of NO+·(H2O)n=4,5 has been hypothesised to involve an intracluster reaction, but no reaction is observed in AIMD simulations using thermal initial velocities. However, it is shown that reactions to form protonated water clusters do occur in simulations when a water molecule collides with a NO+·(H2O)4 cluster.

Accurate and precise ab initio anharmonic free-energy calculations for metallic crystals: Application to hcp Fe at high temperature and pressure

A framework for computing the anharmonic free energy (FE) of metallic crystals using Born-Oppenheimer ab initio molecular dynamics (AIMD) simulation, with unprecedented efficiency, is introduced and demonstrated for the hcp phase of iron at extreme conditions (up to $\ensuremath{\approx}290$ GPa and 5000 K). The advances underlying this work are: (1) A recently introduced harmonically-mapped averaging temperature integration (HMA-TI) method that reduces the computational cost by order(s) of magnitude compared to the conventional TI approach. The TI path starts from zero Kelvin, where it assumes the behavior is given exactly by a harmonic treatment; this feature restricts application to systems that have no imaginary phonons in this limit. (2) A Langevin thermostat with the HMA-TI method that allows the use of a relatively large MD time step (4 fs, which is about eight times larger than the size needed for the Andersen thermostat) without loss of accuracy. (3) AIMD sampling is accelerated by using density functional theory (DFT) with a low-level parameter set, then the measured quantities of selected configurations are robustly reweighted to a higher level of DFT. This introduces a speedup of about 20--$30\ifmmode\times\else\texttimes\fi{}$ compared to directly simulating the accurate system. (4a) The temperature ($T$) dependence of the hcp equilibrium shape (i.e., $c/a$ axial ratio) is determined (including anharmonicity), with uncertainty less than $\ifmmode\pm\else\textpm\fi{}0.001$. (4b) Electronic excitation is included through Mermin's finite-temperature extension of the $T=0$ K DFT. A simple FE perturbation method is introduced to handle the difficulty associated with applying the TI method with a $T$-dependent geometry and (due to electronic excitation) potential-energy surface. (5) The FE in the thermodynamic limit is attained through extrapolation of only the (computationally inexpensive) quasiharmonic FE, because the anharmonic FE contribution has negligible finite-size effects. All methods introduced here do not affect the AIMD sampling---results are obtained through post-processing---so established AIMD codes can be employed without modification. Analytical formulas fitted to the results for the variation of the equilibrium $c/a$ ratio and FE components with $T$ are provided. Notably, effects of magnetic excitations are not included and may yet prove important to the overall FE; if so, it is plausible that such contributions can be added perturbatively to the FE values reported here. Notwithstanding these considerations, FE values are obtained with an estimated accuracy and precision of 2 meV/atom, suggesting that the capability to compute the phase diagram of iron at Earth's inner core conditions is within reach.

Enhancing 4-propylheptane dissociation with nickel nanocluster based on molecular dynamics simulations

In the present work, a 0.4nm nickel cluster has been theoretically studied. Its equilibrium structural parameters have been calculated by the DFT method based on the PBEH1PBE hybrid functional and split-valence basis set Lanl2DZ including effective core potentials. We have systematically considered diverse spin states of this cluster and find out its ground state. The relative stability of these states depends on the HOMO–LUMO gap. The interaction of the Ni6 with 4-propylheptane С10Н22 has been studied to simulate the process of catalytic cracking of hydrocarbons. The optimization of this structure has been performed by the ωPBE/Lanl2DZ_ecp method (the TeraChem V.1.9 program package) with no symmetry restrictions; the electron shells of the metal were described by effective core pseudopotentials. For visualization and quantitative estimation of the bonding bonds between the nickel nanocluster and 4-propylheptane, the analysis of weak interactions based on RGD has been performed. To confirm the proposition about the formation of Ni–H bonds, we have scrutinized critical points of electronic density. Values of laplasian of electronic density and Bader atomic charge distribution in the global minimum of the total energy have been estimated by the AIMAll 15.05.18 program suite. Finally, we have simulated interaction of Ni6 with 4-propylheptane in terms of the Born–Oppenheimer ab initio molecular dynamics. The results of the molecular dynamics simulation provide pair radial distribution function CH at 1500°C and a detailed picture of the processes occurring in the system.

Interfaces Select Specific Stereochemical Conformations: The Isomerization of Glyoxal at the Liquid Water Interface.

Interfacial chemistry involving glyoxal at aerosol surfaces is postulated to catalyze aerosol growth. This chemistry remains speculative due to a lack of detailed information concerning the physicochemical behavior of glyoxal at the interface of atmospheric aerosols. Here, we report results from high-level electronic structure calculations as well as both classical and Born-Oppenheimer ab initio molecular dynamics simulations of glyoxal solvation at the air/liquid water interface. When compared to the gas phase, the trans to cis isomerization of glyoxal at the liquid water interface is found to be catalyzed; additionally, the trans conformation is selectively solvated within the bulk to a greater degree than is the cis conformation. These two processes, i.e., the catalytic effect at the water interface and the differentially selective solvation, act to enhance the concentration of the cis isomer of glyoxal at the water interface. This has important consequences for the interpretation of experiments and for the modeling of glyoxal chemistry both at the interface of water clouds and at aerosols. Broader implications of this work relate to describing the role of interfaces in selecting specific stereo molecular structures at interfacial environments.

Equilibrium Born-Oppenheimer molecular-dynamics exploration of the lattice thermal conductivity of silicon clathrates

Thermal conductivity plays a critical rôle in determining the performance of a thermoelectric material. However, the computation of thermal conductivity from first principles is a challenging and laborious process, with pitfalls galore. Here, we present results on the calculation of the lattice thermal conductivities of silicon clathrates using a very efficient scheme based on the Einstein relationship for the energy moment, sampled from ab initio Born-Oppenheimer molecular dynamics employing linear-scaling Density Functional Theory. Both sI and sII silicon clathrates were studied using systems consisting of up to thousands of atoms. Instead of more glass-like behaviour reported for an empty sII clathrate, the present accurate first-principles calculations predict a thermal-conductivity temperature dependence more in keeping with that of a normal crystal for both clathrates polymorphs, essentially in agreement with a previous theoretical study on sI clathrate. Over the temperature range from 50 to 600K at ambient pressure, it is found that the sI-structure thermal conductivity is somewhat lower than sII, due probably to the greater proportion of larger tetrakaidecahedral 51262 cavities (vis-à-vis smaller dodecahedral 512 cages) therein leading to more substantial dissipation of heat-carrying acoustic phonons. However, the absolute conductivity of sII clathrate is itself limited due to the larger number of atoms per unit cell (136 versus 46 for sI) leading to significant zone-edge damping of acoustic phonons.

Effects of molecular dipole orientation on the exciton binding energy ofCH3NH3PbI3

We present a simple interacting tight-binding model for excitons, which is used to investigate the dependence of the exciton binding energy of ${\mathrm{CH}}_{3}{\mathrm{NH}}_{3}{\mathrm{PbI}}_{3}$ over the disorder induced by the molecular motion at room temperature. The model is fitted to the electronic structure of ${\mathrm{CH}}_{3}{\mathrm{NH}}_{3}{\mathrm{PbI}}_{3}$ by using data from density-functional theory and Born-Oppenheimer ab initio molecular dynamics, and it is solved in the mean-field approximation. When a finite-scale analysis is performed to extract the energetic of the excitons at experimental concentrations we find that disorder in general reduces the binding energy of about 10%. This suggests that the excitonic properties of ${\mathrm{CH}}_{3}{\mathrm{NH}}_{3}{\mathrm{PbI}}_{3}$ largely depend on the electronic structure of the ${\mathrm{PbI}}_{3}$ inorganic lattice.

Hybrid Extended Lagrangian, Post-Hartree-Fock Born-Oppenheimer ab Initio Molecular Dynamics Using Fragment-Based Electronic Structure.

We present a hybrid ab initio molecular dynamics scheme that includes both DFT and Hartree–Fock-based extended Lagrangian and converged post-Hartree–Fock Born–Oppenheimer components, combined within the framework of a molecular fragmentation-based electronic structure. The specific fragmentation algorithm used here is derived from ONIOM but includes multiple, overlapping “model” systems. The interaction between the various overlapping model systems is approximated by invoking the principle of inclusion–exclusion at the chosen higher level of theory and within a “real” calculation performed at the chosen lower level of theory. Furthermore, here, the lower level electronic structure of the full system is propagated through an extended Lagrangian formalism, whereas the fragments, treated using post-Hartree–Fock electronic structure theories, are computed using the normal converged Born–Oppenheimer treatment. This conservative dynamical approach largely reduces the computational cost to approximate on-the-fly...

Ionic Vapor Composition in Critical and Supercritical States of Strongly Interacting Ionic Compounds.

The critical point, CP (T, P), of the phase diagram quantifies the minimum amount of kinetic energy needed to prevent a substance from existing in a condensed phase. Therefore, the CP is closely related to the properties of the fluid far below the critical temperature. Approaches designed to predict thermophysical properties of a system necessarily aim to provide reliable estimates of the CP. Vice versa, CP estimation is impossible without knowledge of the vapor phase behavior. We report ab initio Born-Oppenheimer molecular dynamics (BOMD) simulations of sodium and potassium chlorides, NaCl and KCl, at and above their expected CPs. We advance the present knowledge regarding the existence of ionic species in the vapor phase by establishing significant percentages of atomic clusters: 29-30% in NaCl and 34-38% in KCl. A neutral pair of counterions is the most abundant cluster in the ionic vapors (ca. 35% of all vaporized ions exist in this form). Unexpectedly, an appreciable fraction of clusters is charged. The ionic vapor composition is determined by the vapor density, rather than the nature of the alkali ion. The previously suggested CPs of NaCl and KCl appear overestimated, based on the present simulations. The reported results offer essential insights into the ionic fluid properties and assist in development of thermodynamic theories. The ab initio BOMD method has been applied to investigate the vapor phase composition of an ionic fluid for the first time.

Vibrational and ab initio molecular dynamics studies of bradykinin

In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.

Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.