Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database

An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is an ab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series of ab initio calculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function, etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as “flexible EFP”, is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost

The effect of pi-stacking, h-bonding, and electrostatic interactions on the ionization energies of nucleic acid bases: adenine-adenine, thymine-thymine and adenine-thymine dimers

A combined theoretical and experimental study of the ionized dimers of thymine and adenine, TT, AA, and AT, is presented. Adiabatic and vertical ionization energies(IEs) for monomers and dimers as well as thresholds for the appearance of the protonated species are reported and analyzed. Non-covalent interactions stronglyaffect the observed IEs. The magnitude and the nature of the effect is different for different isomers of the dimers. The computations reveal that for TT, the largestchanges in vertical IEs (0.4 eV) occur in asymmetric h-bonded and symmetric pi- stacked isomers, whereas in the lowest-energy symmetric h-bonded dimer the shiftin IEs is much smaller (0.1 eV). The origin of the shift and the character of the ionized states is different in asymmetric h-bonded and symmetric stacked isomers. Inthe former, the initial hole is localized on one of the fragments, and the shift is due to the electrostatic stabilization of the positive charge of the ionized fragment by thedipole moment of the neutral fragment. In the latter, the hole is delocalized, and the change in IE is proportional to the overlap of the fragments' MOs. The shifts in AAare much smaller due to a less effcient overlap and a smaller dipole moment. The ionization of the h-bonded dimers results in barrierless (or nearly barrierless) protontransfer, whereas the pi-stacked dimers relax to structures with the hole stabilized by the delocalization or electrostatic interactions

Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra

The effect of microhydration on ionization energies of thymine

A combined theoretical and experimental study of the effect of microhydration on ionization energies (IEs) of thymine is presented. The experimental IEs are derived from photoionization efficiency curves recorded using tunable synchrotron VUV radiation. The onsets of the PIE curves are 8.85+-0.05, 8.60+-0.05, 8.55+-0.05, and 8.40+-0.05 eV for thymine, thymine mono-, di-, and tri-hydrates, respectively. The computed (EOM-IP-CCSD/cc-pVTZ) AIEs are 8.90, 8.51, 8.52, and 8.35 eV for thymine and the lowest isomers of thymine mono-, di-, and tri-hydrates. Due to large structural relaxation, the Franck-Condon factors for the 0<-- 0 transitions are very small shifting the apparent PIE onsets to higher energies. Microsolvation strongly affects IEs of thymine -- addition of each water molecule reduces the first vertical IE by 0.10-0.15 eV. The adiabatic IE decreases even more (up to 0.4 eV). The magnitude of the effect varies for different ionized states and for different isomers. For the ionized states that are localized on thymine the dominant contribution to the IE reduction is the electrostatic interaction between the delocalized positive charge on thymine and the dipole moment of the water molecule

Influence of reaction conditions on catalytic properties of rac-Et(2-MeInd)2ZrMe2/(2,6-tBu2PhO-)AliBu2 in ethylene-propylene copolymerization

Ethylene-propylene copolymerization reactions were carried out using rac-Et(2-MeInd)2ZrMe2 catalyst and (2,6-tBu2PhO-)AliBu2 as activator under varying reaction conditions. We demonstrate that reaction conditions such as monomer concentration, Al/Zr molar ratio and solvent type (toluene and heptane) all have significant effect on activity of the system and copolymers composition. The decrease in reaction pressure from 11 to 3 atm leads to: a) 1.6-fold increase in specific activity (from 3030 to 4840 kg copolymer/(mol Zr•h•atm)), b) increase of Mn value from 38 to 89 kg/mol, and c) increase of ethylene content in copolymer from 87 to 92 mol %. The increase of ethylene/propylene molar ratio from 0.7 to 2 does not significantly affect activity but leads to the rise in the ethylene content in copolymer from 92 to 97 mol % and, correspondingly, to the increase of copolymer crystallinity from 43 to 48%. As a result, thermal and mechanical properties of the obtained polymers also change, according to the shifts in copolymers composition. The change in Al/Zr molar ratio is confirmed to have great effect on the catalytic activity of our systems. In a row of Al/Zr= 100, 150, 200, 300 mol/mol, the lowest activity of 80 and the highest one of 8550 kg copolymer/(mol Zr•h•atm) are observed at 100 and 150 molar ratios correspondingly. We have also demonstrated the ability of catalytic systems with isobutylaluminum aryloxide activators to operate in aliphatic medium (heptane). On another note, during the reaction quenching, aryloxide activator hydrolyzes the polymer infused with 2,6-di-tert-butylphenol antioxidant. This results in the increased resistance of copolymers to the thermal-oxidative degradation. The presence of 4 wt% phenol in the copolymer leads to an increase in the 5% mass loss temperature by 67°C. Moreover, increasing the residual phenol content from 2 to 4 wt% affects the mechanical properties of the copolymers: the elongation-at-break increases from 500 to 600%, and the tensile strength decreases from 10 to 8 MPa

Desorption Dynamics, Internal Energies, and Imaging of Organic Molecules from Surfaces with Laser Desorption and Vacuum Ultraviolet (VUV) Photoionization

There is enormous interest in visualizing the chemical composition of organic material that comprises our world. A convenient method to obtain molecular information with high spatial resolution is imaging mass spectrometry. However, the internal energy deposited within molecules upon transfer to the gas phase from a surface can lead to increased fragmentation and to complications in analysis of mass spectra. Here it is shown that in laser desorption with postionization by tunable vacuum ultraviolet (VUV) radiation, the internal energy gained during laser desorption leads to minimal fragmentation of DNA bases. The internal temperature of laser-desorbed triacontane molecules approaches 670 K, whereas the internal temperature of thymine is 800 K. A synchrotron-based VUV postionization technique for determining translational temperatures reveals that biomolecules have translational temperatures in the range of 216-346 K. The observed low translational temperatures, as well as their decrease with increased desorption laser power is explained by collisional cooling. An example of imaging mass spectrometry on an organic polymer, using laser desorption VUV postionization shows 5 mu m feature details while using a 30 mu m laser spot size and 7 ns duration. Applications of laser desorption postionization to the analysis of cellulose, lignin and humic acids are briefly discussed

Advances in Molecular Quantum Chemistry Contained in the Q-Chem 4 Program Package

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube

The supramolecular effect of aromaticity on the crystal packing of furan/thiophene carboxamide compounds

N-2-pyrazinyl-2-furancarboxamide (I) and N-2-pyrazinyl-2-thiophenecarboxamide (II) are compounds containing different five-membered heteroaromatic rings, furan and thiophene, respectively. They were designed and synthesized to examine the effect of an increase in aromaticity from furan to thiophene on the crystal packing. In order to explore the various features of the crystal packing motifs in more detail, single crystal X-ray diffraction, Hirshfeld surface analysis and theoretical calculations were carried out on the two compounds. The results clearly show that the heteroatom substitution of O to S in five-membered rings led to an increase in the effectiveness of π-based interactions in II, whereas hydrogen bond interactions play a more important role in the stabilization of the supramolecular architecture of I