Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

Based on the AMBER polarizable model (ff02), we have re-optimized the parameters related to the main-chain (Phi, Psi) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., beta, P(II), alpha(R), and alpha(L) regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the beta, P(II) and alpha(R) regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)(7)-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization.     

Estimating and modeling charge transfer from the SAPT induction energy

Recent studies using quantum mechanics energy decomposition methods, for example, SAPT and ALMO, have revealed that the charge transfer energy may play an important role in short ranged inter‐molecular interactions, and have a different distance dependence comparing with the polarization energy. However, the charge transfer energy component has been ignored in most current polarizable or non‐polarizable force fields. In this work, first, we proposed an empirical decomposition of SAPT induction energy into charge transfer and polarization energy that mimics the regularized SAPT method (ED‐SAPT). This empirical decomposition is free of the divergence issue, hence providing a good reference for force field development. Then, we further extended this concept in the context of AMOEBA polarizable force field, proposed a consistent approach to treat the charge transfer phenomenon. Current results show a promising application of this charge transfer model in future force field development. © 2017 Wiley Periodicals, Inc.     

Microwave‐assisted synthesis of 2‐(2‐pyridyl)azoles. Study of their corrosion inhibiting properties

An efficient and fast procedure for the synthesis of 2‐(2‐pyridyl)azoles is described using ionic liquids as catalysts under microwave irradiation. The X‐ray crystallographic analyses for three of the four synthesized compounds are presented. Potentiodynamic polarization studies were carried out to analyze the electrochemical behavior of the compounds in corrosive acidic media. Of the four derivatives, one compound was detected to be an effective corrosion inhibitor prototype for oil refinery environments.     

Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of Förster theory

In the present study, the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C‐phycocyanin (C‐PC) were investigated in term of the Förster theory. The corresponding excited states and transition dipole moments of phycocyanobilins (PCBs) located into C‐PC were examined by model chemistry in gas phase at time‐dependent density functional theory (TDDFT), configuration interaction‐singles (CIS), and Zerner's intermediate neglect of differential overlap (ZINDO) levels, respectively. Then, the long‐range pigment‐protein interactions were approximately taken into account by using polarizable continuum model (PCM) at TDDFT level to estimate the influence of protein environment on the preceding calculated physical quantities. The influence of the short‐range interaction caused by aspartate residue nearby PCBs was examined as well. Only when the protonation of PCBs and its long‐ and short‐range interactions were properly taken into account, the calculated energy transfer rates (1/K) in the framework of Förster model at TDDFT/B3LYP/6‐31+G* level were in good agreement with the experimental results of C‐PC monomer and trimer. Furthermore, the present calculated results suggested that the energy transfer pathway in C‐PC monomer is predominant from β‐155 to β‐84 (1/K = 13.4 ps), however, from α‐84 of one monomer to β‐84 (1/K = 0.3–0.4 ps) in a neighbor monomer in C‐PC trimer. In C‐PC hexamer, an additional energy flow was predicted to be from β‐155 (or α‐84) in top trimer to adjacent β‐155 (or α‐84) (1/K = 0.5–2.7 ps) in bottom trimer. © 2013 Wiley Periodicals, Inc.     

Study of the temperature‐dependent conformational averaging of 1H NMR resonances in vinylcyclopropane through the use of ab initio methodology and Boltzmann statistics

The temperature dependence of the ¹ H NMR resonance of the C‐4 olefinic proton in vinylcyclopropane was investigated through a combination of ab initio calculations and Boltzmann statistics. A torsional energy profile as a function of the 〈?〉 dihedral angle was obtained using HF methodology with a 6–311G** basis set, while the corresponding ¹ H chemical shift profiles for the C‐4 proton were computed using the GIAO approach and either HF, DFT (B3LYP) or MP2 methods at the 6–311G** level of theory. Chemical shifts at different temperatures calculated as canonical ensemble averages in which the different ab initio ¹ H chemical shift profiles and a Boltzmann factor defined by the HF/ 6–311G** energy function are employed reproduce remarkably well the temperature dependence observed experimentally. Attempts to perform a similar study using only the GIAO‐MP2 ¹ H chemical shift profile and 〈?〉 dihedral angle trajectories obtained from molecular dynamics simulations at different temperatures failed to reproduce the experimental trends. This shortcoming was attributed to the inability of the force fields employed, Tripos 6.0 and MMFF94, to reproduce properly the three‐well torsional potential of vinylcyclopropane. The application of both methodologies to the calculation of population‐dependent chemical shifts in other systems is discussed. Copyright © 2002 John Wiley & Sons, Ltd.     

Femtochemistry of trans‐Azomethane: A Combined Experimental and Theoretical Study

The dissociation dynamics of trans‐azomethane upon excitation to the S₁(n,π*) state with a total energy of 93 kcal mol^?1 is investigated using femtosecond‐resolved mass spectrometry in a molecular beam. The transient signal shows an opposite pump–probe excitation feature for the UV (307 nm) and the visible (615 nm) pulses at the perpendicular polarization in comparison with the signal obtained at the parallel polarization: The one‐photon symmetry‐forbidden process excited by the UV pulse is dominant at the perpendicular polarization, whereas the two‐photon symmetry‐allowed process initiated by the visible pulse prevails at the parallel polarization. At the perpendicular polarization, we found that the two C? N bonds of the molecule break in a stepwise manner, that is, the first C? N bond breaks in ≈70 fs followed by the second one in ≈100 fs, with the intermediate characterized. At the parallel polarization, the first C? N bond cleavage was found to occur in 100 fs with the intensity of the symmetry‐allowed transition being one order of magnitude greater than the intensity of the symmetry‐forbidden transition at the perpendicular polarization. Theoretical calculations using time‐dependent density functional theory (TDDFT) and the complete active space self‐consistent field (CASSCF) method have been carried out to characterize the potential energy surface for the ground state, the low‐lying excited states, and the cationic ground state at various levels of theory. Combining the experimental and theoretical results, we identified the elementary steps in the mechanism: The initial driving force of the ultrafast bond‐breaking process of trans‐azomethane (at the perpendicular polarization) is due to the CNNC torsional motion initiated by the vibronic coupling through an intensity‐borrowing mechanism for the symmetry‐forbidden n–π* transition. Following this torsional motion and the associated molecular symmetry breaking, an S₀/S₁ conical intersection (CI) can be reached at a torsional angle of 93.1° (predicted at the CASSCF(8,7)/cc‐pVDZ level of theory). Funneling through the S₀/S₁ CI could activate the asymmetric C? N stretching motion, which is the key motion for the consecutive C? N bond breakages on the femtosecond time scale.     

A novel decomposition of torsional potentials into pairwise interactions: A study of energy second derivatives

A general method of analyzing intramolecular torsional potentials in terms of energy second derivatives that couple the rotating atoms is presented. The method offers a rigorous decomposition of the total torsional potential into pairwise (dihedral) interactions and enables one to derive nonbonded torsional interactions between 1–4 atoms as well as between more distant atoms and sites. The method is demonstrated on ethane, propane and acetaldehyde. It is shown that the 1–4 H…H dihedral potentials in ethane and propane are very similar, thereby supporting the notion of transferable force field potential functions. However, the dihedral potentials that are obtained differ from 1–4 potentials that are used in current force fields. Intramolecular three body effects are clearly seen in this method and are found to be relatively large for the dihedral interactions, although in the one case studied (propane) the overall effect on the methyl-methyl interaction is negligible due to cancellation of terms. The analysis explicitly shows that the barrier in acetaldehyde is due mainly to the dihedral H…H interaction.     

On a semiclassical interpretation of inter- and intramolecular interactions

The semiclassical models considered here are composed by charge distributions coming from ab initio quantum-mechanical calculations on actual molecular systems. These charge distributions interact with one another according to the laws of classical electrostatics. This article describes some results of a systematic examination of the performances of this model in a variety of cases, with the aim of putting in evidence the usefulness and the limits of this inherently approximate representation of chemical interactions. Intermolecular interactions are examined first; the test cases are interactions of neutral molecules with H⁺, Li⁺, and C1^?, and the formation of H-bonded complexes. Attention is paid mainly to the energetics of the processes; each interacting molecule is considered as a unique entity and classical molecular reactivity indexes (electrostatic potential V, polarization term P) are introduced to compute the interaction energy, to interpret the details of the interaction process, and then to elaborate on less expensive computational procedures. Intramolecular interactions are considered. Attention is paid to the question of defining chemical groups starting from SCF molecular wavefunctions. The transferability and conservation degree of groups derived from localized orbitals of actual molecules is examined in detail, taking as tests their ability to reproduce charge distribution, one-electron observables, and energy. The effect of classical fields on these groups is then examined, taking into consideration external fields originated either by a point charge or by a solvent, and internal fields deriving from substitution of chemical groups. The intergroup analysis is then extended to the case of bimolecular reaction acts by considering the whole system as a supermolecule. Approximate computational procedures able to reproduce the main features of these interactions are proposed and tested. All through the article the performances of the classical models are compared with ab initio SCF calculations (mainly of low or intermediate quality).     

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein-protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson-Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos-c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos-c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.     

Polarizable Atomistic Calculation of Site Energy Disorder in Amorphous Alq3

A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8‐hydroxyquinolinato)aluminum (Alq₃) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight‐binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq₃ and the effect of the polarization on the site energy disorder is discussed.     

Limitations of Global Hybrids in Predicting the Geometries and Torsional Energy Barriers of Dimeric Systems and the Role of Hartree Fock and DFT Exchange

Prediction of accurate geometries is a prerequisite for accurate prediction of molecular properties. Impact of Hartree Fock (HF) exchange (a₀) on geometry in the framework of DFT is investigated by monitoring dihedral angles, bond length alternations, and torsional energy barriers of 10 dimeric systems against CCSD (ADZ/ATZ) benchmarks. A strong correlation is observed between the fraction of HF exchange, equilibrium dihedral angles, and the potential energy barriers in global hybrids. Full HF exchange is critical to accurately predict the nonplanarity. Lower fractions of (a₀)/larger DFT exchange (1-a₀) results in overestimation of torsional energy barriers at 90⁰ and underestimation at 0⁰. Large contributions of (1-a₀) in global hybrid functionals tend to overestimate torsional energy barriers (90⁰) and are biased toward planar geometries. However, inclusion of larger fractions of (a₀)/lower (1-a₀) also overestimate the torsional energy barriers in syn-conformations due to the localization errors associated with HF exchange in global hybrids. Hence, irrespective of the fraction of HF/DFT exchange incorporated, global hybrids fail to accurately predict torsional energy barriers at 0⁰ and 90⁰ simultaneously. Long-range corrected (LC) functionals, which employ full HF exchange at longer regions, outperform global hybrid functionals in predicting geometries and torsional energy barriers of the dimeric molecules. The distance dependence of (a₀) thus provides a balanced fraction of HF exchange as the dihedral torsion varies. Impact of range separation parameter on geometries is marginal in altering the planarity/nonplanarity. However, range separation parameter within 0.20–0.40 bohr⁻¹ predicts more reliable torsional energies and geometries. © 2019 Wiley Periodicals, Inc.     

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short‐range penetration correction up to quadrupoles

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short‐range charge penetration correction modifying the charge‐charge, charge‐dipole and charge‐quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry‐Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono‐ and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER‐HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration‐corrected polarizable force fields highlighting the mandatory need of non‐spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short‐range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio‐ or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.     

Molecular dynamics study of polarizable point dipole models for molten sodium iodide

The structure, the ionic transport properties, and the dynamics of long-wavelength charge-density fluctuations, for two polarizable point dipole models of molten NaI, have been studied by molecular dynamics simulations. These models are based on a rigid ion potential to which the induced dipole polarization of the anions is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and short-range damping interactions that oppose the electrically induced dipole moments. The two polarizable ion models differ only in the range of the damping polarization interactions. The influence of the induced anion polarization on the different properties of simulated molten NaI is discussed.     

Two different modes of halogen bonding in two 4‐nitroimidazole derivatives

In the crystal structures of the two imidazole derivatives 5‐chloro‐1,2‐dimethyl‐4‐nitro‐1H‐imidazole, C₅H₆ClN₃O₂, (I), and 2‐chloro‐1‐methyl‐4‐nitro‐1H‐imidazole, C₄H₄ClN₃O₂, (II), C—Cl...O halogen bonds are the principal specific interactions responsible for the crystal packing. Two different halogen‐bond modes are observed: in (I), there is one very short and directional C—Cl...O contact [Cl...O = 2.899 (1) Å], while in (II), the C—Cl group approaches two different O atoms from two different molecules, and the contacts are longer [3.285 (2) and 3.498 (2) Å] and less directional. In (I), relatively short C—H...O hydrogen bonds provide the secondary interactions for building the crystal structure; in (II), the C—H...O contacts are longer but there is a relatively short π–π contact between molecules related by a centre of symmetry. The molecule of (I) is almost planar, the plane of the nitro group making a dihedral angle of 6.97 (7)° with the mean plane of the imidazole ring. The molecule of (II) has crystallographically imposed mirror symmetry and the nitro group lies in the mirror plane.