Kernel energy method illustrated with peptides

We describe a kernel energy method (KEM) for applying quantum crystallography to large molecules, with an emphasis on the calculation of the molecular energy of peptides. The computational difficulty of representing the system increases only modestly with the number of atoms. The calculations are carried out on modern parallel supercomputers. By adopting the approximation that a full biological molecule can be represented by smaller “kernels” of atoms, the calculations are greatly simplified. Moreover, collections of kernels are, from a computational point of view, well suited for parallel computation. The result is a modest increase in computational time as the number of atoms increases, while retaining the ab initio character of the calculations. We describe a test of our method, and establish its accuracy using 15 different peptides of biological interest. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.     

Conformer-independent ureidoimidazole motifs--tools to probe conformational and tautomeric effects on the molecular recognition of triply hydrogen-bonded heterodimers

Linear arrays of hydrogen bonds are useful for the reversible assembly of “stimuli‐responsive” supramolecular materials. There is thus an ongoing requirement for easy‐to‐synthesise motifs that are capable of presenting hydrogen‐bonding functionality in a predictable manner, such that high‐affinity and high‐fidelity recognition occurs. The design of linear arrays is made challenging as a consequence of their ability to adopt multiple conformational and tautomeric configurations; with each additional hydrogen‐bonding heteroatom added to an array, the available tautomeric and conformational space increases and it can be difficult to anticipate where unproductive conformers/tautomers will arise. This paper describes a detailed study on the complementary ureidoimidazole donor–donor–acceptor (DDA) array ( 1 ) and amidoisocytosine donor–acceptor–acceptor (DAA) array ( 2 ). A specific feature of 1 is that two degenerate, intramolecular hydrogen‐bonded conformations are postulated, both of which present a DDA array that is complementary to appropriate DAA partners. 1D and 2D ¹H NMR spectroscopy, isothermal titration calorimetry, and ab initio structure calculations confirm 1 interacts with 2 (K_a≈33000 M ^?1 in CDCl₃) in a conformer‐independent fashion driven by enthalpy. Comparison of the binding behaviour of 1 with hexylamidocytosine ( 4 ) and amidonaphthyridine ( 5 ) provides insight on the role that intramolecular hydrogen‐bonding plays in mediating affinity towards DAA partners.     

Ab initio molecular dynamics using hybrid density functionals

Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.     

Local Disorder in Hydrogen Storage Compounds: The Case of Lithium Amide/Imide

Amides and imides of alkali metals are a very promising class of materials for use as a hydrogen‐storage system, as they are able to store and release hydrogen via a chemical route at controllable temperatures and pressures. We critically revise the present picture of the atomic structure of the lightest member (LiNH₂/Li₂NH) by using a combined computational and experimental approach. Specifically, ab initio path integral molecular dynamics simulations and solid‐state ¹H NMR techniques are combined. The results show that the presently assumed local structure might be inconsistent or at least incomplete and needs considerable revision. In particular, the Li atoms turn out to be more mobile and more disordered than suggested by structural data obtained from X‐ray scattering. Also, the configuration of the hydrogen atoms, which is accessible via the NMR experiment and the corresponding first‐principles calculations, is different from the previously assumed data. The computed and experimentally observed ¹H NMR parameters are in very good mutual agreement and illustrate the unusual chemical environment of the hydrogen atoms in this system. Incorporating our results on the new lithium data, we show that the effect of nuclear quantum delocalization for the hydrogen atoms is considerably reduced compared to the perfect crystal structure.     

Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF,MP2, DFT,and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory

At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-structure determinations in silico methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311++G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311++G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311+G(d,p)//B3LYP/6-311++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.     

Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?

Halogenated compounds are gaining an increasing importance in medicinal chemistry and materials science. Ab initio quantum chemistry (QC) has unraveled the existence of a “sigma hole” along the C? X (X = F, Cl, Br, I) bond, namely, a depletion of electronic density prolonging the bond, concomitant with a build‐up on its sides, both of which are enhanced along the F < Cl < Br < I series. We have evaluated whether these features were intrinsically built‐in in an anisotropic, polarizable molecular mechanics (APMM) procedure such as SIBFA (sum of interactions between fragments ab initio computed). For that purpose, we have computed the interaction energies of fluoro‐, chloro‐, and bromobenzene with two probes: a divalent cation, Mg(II), and water approaching X through either one H or its O atom. This was done by parallel QC energy‐decomposition analyses (EDA) and SIBFA computations. With both probes, the leading QC contribution responsible for the existence of the sigma hole is the Coulomb contribution E_c. For all three halogenated compounds, and with both probes, the in‐ and out‐of‐plane angular features of E_c were closely mirrored by the SIBFA electrostatic multipolar contribution (E_MTP). Resorting to such a contribution thus dispenses with empirically‐fitted “extra”, off‐centered partial atomic charges as in classical molecular mechanics/dynamics. © 2013 Wiley Periodicals, Inc.     

Efficient “On‐the‐Fly” calculation of Raman Spectra from Ab‐Initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water

We present a novel computational method to accurately calculate Raman spectra from first principles. Together with an extension of the second‐generation Car‐Parrinello method of Kühne et al. (Phys. Rev. Lett. 2007, 98, 066401) to propagate maximally localized Wannier functions together with the nuclei, a speed‐up of one order of magnitude can be observed. This scheme thus allows to routinely calculate finite‐temperature Raman spectra “on‐the‐fly” by means of ab‐initio molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra. © 2015 Wiley Periodicals, Inc.     

Modeling electrochemical interfaces from ab initio molecular dynamics: water adsorption on metal surfaces at potential of zero charge

The origin of the potential difference between the potential of zero charge of a metal/water interface and the work function of the metal is a recurring issue because it is related to how water interacts with metal surface in the absence of surface charge. Recently ab initio molecular dynamics method has been used to model electrochemical interfaces to study interfacial potential and the structure of interface water. Here, we will first introduce the computational standard hydrogen electrode method, which allows for ab initio determination of electrode potentials that can be directly compared with experiment. Then, we will review the recent progress from ab initio molecular dynamics simulation in understanding the interaction between water and metal and its impact on interfacial potential. Finally, we will give our perspective for future development of ab initio computational electrochemistry.     

Decomposing total IR spectra of aqueous systems into solute and solvent contributions: a computational approach using maximally localized Wannier orbitals

The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.     

A concerted approach for the determination of molecular conformation in ordered and disordered materials

We present the successful application of a concerted approach for the investigation of the local environment in ordered and disordered phases in the solid state. In this approach we combined isotope labeling with computational methods and different solid-state NMR techniques. We chose triphenylphosphite (TPP) as an interesting example of our investigations because TPP exhibits two crystalline modifications and two different amorphous phases one of which is highly correlated. In particular we analyzed the conformational distribution in three of these phases. A sample of triply labeled 1-[13C]TPP was prepared and 1D MAS as well as wide-line 13C NMR spectra were measured. Furthermore we acquired 2D 13C wide-line exchange spectra and used this method to derive highly detailed information about the phenyl orientation in the investigated TPP phases. For linkage with a structure model a DFT analysis of the TPP molecule and its immediate environment was carried out. The ab initio calculations of the 13C chemical shift tensor in three- and six-spin systems served as a base for the calculation of 1D and 2D spectra. By comparing these simulations to the experiment an explicit picture of all phases could be drawn on a molecular level. Our results therefore reveal the high potential of the presented approach for detailed studies of the mesoscopic environment even in the challenging case of amorphous materials.     

The Transannular Interaction in [2.2]Paracyclophane: Repulsive or Attractive?

The molecular structure and charge density distribution in the crystal of [2.2]paracyclophane derived from the high‐resolution single crystal X‐ray diffraction data at 100 K is reported together with ab initio calculations of this molecule. Analysis of the atomic, anisotropic displacement parameters in a “rigid‐body” model approximation has revealed that the molecule is ordered in the crystal. Topological analysis of the electron density and potential‐energy density‐distribution functions has demonstrated that there is no “through‐space” interaction between the rings in the molecule. The role of the ethylene bridges and distortion of the aromatic desks on the inter‐ring interaction are discussed.     

Activity difference between alpha-COOH and beta-COOH in N-phosphorylaspartic acids

N-phosphorylamino acids are chemically active species that have many biomimic activities. alpha-COOH in amino acids and peptides behaviors rather differently than beta-COOH in many biochemical processes and takes a more important role in the origin of life. Activity differences between alpha-COOH and beta-COOH in the peptide formation of phosphoryl amino acids are studied by 1D, 2D NMR techniques and by ab initio and density functional theory (DFT) calculations in this paper. Phosphoryl dipeptide is formed directly from phosphoryl aspartic acids without any coupling reagents. Only the alpha-dipeptide ester is observed by 1D (1)H, (13)C, and (31)P NMR and 2D NMR. In the ab initio and DFT calculations, the pentacoordinate phosphorane intermediates containing five-membered rings are predicted to be more favored than those with six-membered rings. Both the experimental results and the theoretical calculations suggest that only the alpha-COOH group is activated by N-phosphorylation in N-phosphorylaspartic acid under mild conditions.     

Accurate density functional theory description of binding constants and NMR chemical shifts of weakly interacting complexes of C60 with corannulene‐based molecular bowls

Density functional calculations on “catch and release” complexes of C₆₀ with corannulene derived molecular bowls show that computationally obtained ¹H nuclear magnetic resonance (NMR) chemical shifts can be used as a reliable predictor of binding constants. A wide range of functionals was benchmarked against accurate ab initio calculations to ensure a credible representation of the weak forces that dominate the interactions in these systems. The most reliable density functional theory (DFT) results were then calibrated using experimentally observed NMR data. Careful analysis and comparison of a wide range of commonly used density functionals shows that the explicit inclusion of dispersion corrections is currently the only reliable way to accurately describe the systems investigated in our study. Moreover, we are able to show that the B97‐D and ωB97X‐D functionals are not only able to reproduce ab initio benchmark calculations, but they do so accurately with a moderately sized basis sets and without the problems of numerical integration we encountered with other functionals in this study. © 2013 Wiley Periodicals, Inc.     

Structural characterization of poly(diethylsiloxane) in the crystalline, liquid crystalline and isotropic phases by solid-state 17O NMR spectroscopy and ab initio MO calculations

The structure of poly(diethylsiloxane) (PDES) has been characterized using solid-state NMR of (17)O. The sample studied had a weight-average molecular weight of 2.45 x 10(5). The sample was prepared by utilizing the cationic ring-opening polymerization of (17)O-enriched hexacyclotrisiloxane. Solid-state NMR of (17)O-enriched PDES was measured on the low-temperature beta(1) phase, the high-temperature beta(2) phase, the two-phase system consisting of the liquid crystal and isotropic liquid phase and the isotropic phase. From these data, the molecular structure and dynamics of PDES in the various phases were characterized via the chemical shifts of (17)O, and electric field gradient parameters were determined from NMR and ab initio molecular orbital (MO) calculations. In addition to the solid-state NMR of (1)H, (13)C and (29)Si previously reported on these samples, knowledge of the dynamic behavior of PDES as inferred from the NMR of (17)O in the present study was enhanced significantly. Further, the potential of combining the experimental NMR of (17)O with ab initio MO calculations to characterize the dynamics of polymers containing oxygen is demonstrated.     

溴代1-己基-3-甲基咪唑离子液体与丙酮的相互作用

1H and 13C NMR chemical shifts were determined to investigate the interactions of acetone with a room temperature ionic liquid 1-hexyl-3- methylimidazolium bromide C6mimBr at various mole fractions. Changes in chemical shifts of hydrogen nuclei and of carbon nuclei with the acetone concentration indicated the formation of hydrogen bond between anion of the ionic liquid and methyl protons of acetone. The NMR results were in good agreement with the ab initio computational results.     

Noncollinear spin density functional theory for spin‐frustrated and spin‐degenerate systems

We have implemented ab initio linear combinations of Gaussian‐type orbital calculations with generalized localized spin density approximation (GLSDA) for a dimer of equilateral H₃ as a model of the noncollinear magnetic clusters. It has been found that the GLSDA solution with the three‐dimensional noncollinear spin structure is, contrary to prior band calculations by other groups, the ground state near the O_h conformation. Further computational results are compared to that of ab initio generalized Hartree–Fock. The difference between them and the influence of the correlation correction were discussed. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001