GALAMOST: GPU‐accelerated large‐scale molecular simulation toolkit

GALAMOST [graphics processing unit (GPU)‐accelerated large‐scale molecular simulation toolkit] is a molecular simulation package designed to utilize the computational power of GPUs. Besides the common features of molecular dynamics (MD) packages, it is developed specially for the studies of self‐assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by using some lately developed simulation techniques. To accelerate the simulations, GALAMOST contains a hybrid particle‐field MD technique where particle–particle interactions are replaced by interactions of particles with density fields. Moreover, the numerical potential obtained by bottom‐up coarse‐graining methods can be implemented in simulations with GALAMOST. By combining these force fields and particle‐density coupling method in GALAMOST, the simulations for polymers can be performed with very large system sizes over long simulation time. In addition, GALAMOST encompasses two specific models, that is, a soft anisotropic particle model and a chain‐growth polymerization model, by which the hierarchical self‐assembly of soft anisotropic particles and the problems related to polymerization can be studied, respectively. The optimized algorithms implemented on the GPU, package characteristics, and benchmarks of GALAMOST are reported in detail. © 2013 Wiley Periodicals, Inc.     

The ground state of TiC revisited

The ground state of TiC is ³⁺, as predicted by previous configuration interaction calculations. It is shown that there are two low-lying ¹⁺ states and that the density functional theory solution corresponds to the higher of the two ¹⁺ states.Contribution to the Björn Roos Honorary Issue     

Multipolar electrostatics for proteins: Atom–atom electrostatic energies in crambin

Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom‐atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom‐atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ?_A+ ?_B + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom‐atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug‐cc‐pVTZ and MP2/aug‐cc‐pVTZ levels are only slightly larger than those calculated at HF/6‐31G(d,p) level. This convergence behavior is transferable to the well‐known amyloid beta polypeptide Aβ_1–42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance. © 2013 Wiley Periodicals, Inc.     

Rapid parameterization of small molecules using the force field toolkit

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide‐scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM‐compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure‐solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). © 2013 Wiley Periodicals, Inc.     

A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Prostaglandin H synthase catalyzes the oxygenation of arachidonic acid into the cyclic endoperoxide, prostaglandin G₂ (PGG₂), and the subsequent reduction of PGG₂ to the corresponding alcohol, prostaglandin H₂ (PGH₂), the precursor of all prostaglandins and thromboxanes. Both radical abstraction by a neighboring tyrosyl radical and combined radical/carbocationic models have been proposed to explain the cyclooxygenase part of this reaction. We have used density functional theory calculations to study the mechanism of the formation of the cyclooxygenated product PGG₂. We found an activation free energy for the initial hydrogen abstraction by the tyrosine radical of 15.6 kcal/mol, and of 14.5 kcal/mol for peroxo bridge formation, in remarkable agreement with the experimental value of 15.0 kcal/mol. Subsequent steps of the radical-based mechanism were found to happen with smaller barriers. A combined radical/carbocation mechanism proceeding through a sigmatropic hydrogen shift was ruled out, owing to its much larger activation free energy of 36.5 kcal/mol. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0476-9. Electronic Supplementary MaterialSupplementary material is available in the online version of this article at Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

Expanded Ligands Based upon Iron(II) Coordination Compounds of Asymmetrical Bis(terpyridine) Domains

The synthesis and characterization of two tritopic ligands containing a 2,2′:6′,2″-terpyridine (tpy) metal binding domain and either a 3,2′:6′,3″- or a 4,2′:6′,4″-tpy domain are detailed. The synthetic routes to these ligands involved the [Pd(dppf)Cl₂]-catalyzed coupling of a boronic ester-functionalized 2,2′:6′,2″-tpy with bromo-derivatives of 3,2′:6′,3″-tpy or 4,2′:6′,4″-tpy. The 2,2′:6′,2″-tpy domains of the tritopic ligands preferentially bind Fe²⁺ in reactions with iron(II) salts leading to the formation of two homoleptic iron(II) complexes containing two peripheral 3,2′:6′,3″-tpy or 4,2′:6′,4″-tpy metal-binding sites, respectively. These iron(II) complexes are potentially tetratopic ligands and represent expanded versions of tetra(pyridin-4-yl)pyrazine.     

LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library

A new high performance parallel implementation of the general Effective Fragment Potential (EFP) method in a form of a portable software library called libefp is presented. The libefp library was designed to provide developers of various quantum chemistry software packages with an easy way to add EFP functionality to the program of their choice. The general overview of the library is presented and various aspects of interfacing the library with third party quantum chemistry packages are considered. The reference implementation of common methods of computational chemistry such as geometry optimization and molecular dynamics on top of libefp is delivered in the form of efpmd program. Results of molecular dynamics simulation of liquid water using the developed software are described. © 2013 Wiley Periodicals, Inc.     

Siliciumhaltige spirocyclische Phosphor(V)-Hydrazin-Heterocyclen

Silicon-Containing Spirocyclic Phosphorus(V) Hydrazine Heterocycles In the reaction of 1,1-dichlorosilacyclohexane with dihydrazido thiophosphoric acid O-phenylester in a 1:1 molar ratio in THF as solvent and in the presence of triethylamine mainly the expected spirocyclic system of inorganic and organic heterocycle is formed with the Si atom as spirocenter (ms, nmr). In addition and in low yield crystalls of a dimeric compound are isolated. A single crystall x-ray analysis reveals this compound to consist of a dispiro system with a central centrosymmetric eightmembered inorganic heterocycle connected with two silacyclohexanes via Si spirocenters.     

Bond length alternation in ground and HOMO→LUMO excited states in polyenes. Dynamic Stokes shift?

Complete-active-space self-consistent-field calculation of the reorganisation energy, , corresponding to the strongly allowed HOMOLUMO transition in planar polyenes in the trans form (C _{2 h} symmetry), gives >0.5 eV. This large depends on the fact that the short and long bond lengths of the excited ¹B _u (or ³B _u ) state compared to the ¹A _g ground state are almost cancelled. The emission redshift (Stokes shift) in molecules with the same type of system is quite small, however, which suggests that the Stokes shift may be dynamic, owing to the presence of another excited state at lower or about the same energy. Acknowledgement.We congratulate Björn on his birthday and at the same time thank him for the CASSCF method and for many years of collaboration and help from him and his collaborators to make this wonderful method work in our laboratory.Contribution to the Björn Roos Honorary Issue     

A combined semiempirical and DFT computational protocol for studying bioorganometallic complexes: Application to molybdocene–cysteine complexes

Computational methods can help in the design of new bioorganometallic compounds. However, the presence of multihapto or σ/π metal‐ligand bonding still precludes the direct application of either pure molecular mechanics (MM) or hybrid quantum mechanics‐MM methods to study the flexibility of biomolecules in complex with organometallics. Herein, we present a computational protocol aimed to the evaluation of the relative free energies of bioorganometallic compounds, which explores the conformational space by means of Molecular Dynamics simulations using the semiempirical PM6 method coupled with the COnductor‐like Screening MOdel solvation model followed by density functional theory (DFT) calculations including the DFT‐D3 dispersion energy correction on the most stable conformers. This protocol is applied to investigate the complexes formed between cysteine and the molybdocene entity Cp₂Mo²⁺ (Cp?η⁵? C₅H₅), which has received considerable attention due to its potential antitumor activity and chemical reactivity. The calculated structures and free energies are in agreement with those of the experimentally detected molybdocene‐cysteine adducts and allow us to investigate the reaction mechanism for the formation of the most stable 1:1 and 1:2 adducts. © 2013 Wiley Periodicals, Inc.     

The performance of density functional theory for LnF (Ln=Nd,Eu, Gd,Yb) and YbH

Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue     

Why do molecules echo atomic periodicity?

Franck–Condon factors are investigated for sequences of free main‐group diatomic molecules. Theory‐based Condon loci (parabolas) and Morse‐potential loci are plotted on Deslandres tables to verify if they, indeed, follow the largest Franck–Condon factors. Then, the inclination angles of the Condon loci are determined. Thus, entire band systems are quantified by one variable, the angle. For all available isoelectronic sequences, this angle increases from a central minimum toward magic‐number molecular boundaries. The theory for the Condon locus gives the angle in terms of the ratio of the upper‐state to the lower‐state force constants. It is concluded that the periodicity is caused due to the fact that this ratio becomes larger as rare‐gas molecules are approached, a trend that probably points to the extreme cases of the rare‐gas molecules themselves. Thus, molecular periodicity echoes atomic periodicity in that data plots have extrema at molecules with magic‐number atoms, yet it does not echo the details of atomic periodicity in series between those molecules. © 2013 The Authors. International Journal of Quantum Chemistry Published by Wiley Periodicals, Inc.     

Dynamics and structural changes of small water clusters on ionization

Despite utmost importance in understanding water ionization process, reliable theoretical results of structural changes and molecular dynamics (MD) of water clusters on ionization have hardly been reported yet. Here, we investigate the water cations [(H₂O)_{n = 2–6}⁺] with density functional theory (DFT), Möller–Plesset second‐order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The complete basis set limits of interaction energies at the CCSD(T) level are reported, and the geometrical structures, electronic properties, and infrared spectra are investigated. The characteristics of structures and spectra of the water cluster cations reflect the formation of the hydronium cation moiety (H₃O⁺) and the hydroxyl radical. Although most density functionals fail to predict reasonable energetics of the water cations, some functionals are found to be reliable, in reasonable agreement with high‐level ab initio results. To understand the ionization process of water clusters, DFT‐ and MP2‐based Born‐Oppenheimer MD (BOMD) simulations are performed on ionization. On ionization, the water clusters tend to have an Eigen‐like form with the hydronium cation instead of a Zundel‐like form, based on reliable BOMD simulations. For the vertically ionized water hexamer, the relatively stable (H₂O)₅⁺ (5sL4A) cluster tends to form with a detached water molecule (H₂O). © 2013 Wiley Periodicals, Inc.     

Systematic convergence of energies with respect to basis set and treatment of electron correlation: focal-point conformational analysis of methanol

A practical means of overcoming the limitation in accuracy of conformational analysis due to incompleteness of basis sets used in ab initio calculations involves calculating the energy with a series of systematically improving basis sets and extrapolating to the basis set limit. We report here a focal-point conformational analysis for methanol. The Hartree–Fock energy converges exponentially to the basis set limit, while the convergence of second-order correlation energy is well described by the formula . This formula also describes well the convergence of fourth-order correlation energy. The height of the rotational barrier at the Hartree–Fock level can be obtained reliably by taking the difference of the extrapolated energies of the two conformations and correcting the difference for correlation effects. Electron correlation has only a small decreasing effect on the height of the rotational barrier in methanol. The focal-point value for the torsional barrier in methanol is 0.999±0.007 kcal/mol. Acknowledgement.This project was supported by Provost Funds at University of California, Santa Barbara (UCSB). The computational resources were provided partially by the National Computational Science Alliance and UCSBs Supercomputer Facility. We also acknowledge the Horgan Award (University of Missouri-Columbia) to K. K., which made possible the purchase of additional computational resources. We thank Robert Gdanitz and Bernie Kirtman for valuable discussions and Jozef Noga for providing us with a copy of the DIRCCR12-OS program.     

New structural parameters of fullerenes for principal component analysis

The Kekulé structure count and the permanent of the adjacency matrix of fullerenes are related to structural parameters involving the presence of contiguous pentagons p, q, r, q/p and r/p, where p is the number of edges common to two pentagons, q is the number of vertices common to three pentagons and r is the number of pairs of nonadjacent pentagons adjacent to another common pentagon. The cluster analysis of the structural parameters allows classification these parameters. Principal component analysis (PCA) of the structural parameters and the cluster analyses of the fullerenes permit their classification. PCA clearly distinguishes five classes of fullerenes. The cluster analysis of fullerenes is in agreement with PCA classification. Cluster analysis shows greatest similarity for the q–q/p and r–r/p pairs. PCA provides five orthogonal factors F ₁–F ₅. The use of F ₁ gives an error of 28%. The inclusion of F ₂ decreases the error to 2%.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002)     

Ab initio and density functional studies on the structure and vibrational spectra of 2-hydroxy-1,4-naphthoquinone-1-oxime derivatives

Structure and vibrational frequencies of lawsoneoxime and its C₃-substituted (R=CH₃, NH₂, Cl, NO₂) derivatives in keto and nitrosophenol forms have been obtained employing the Hartree–Fock and density functional methods. Charge distributions in different conformers have been studied using the molecular electrostatic potential topography as a tool. For all these derivatives except for nitrolawsoneoxime the amphi conformer in the keto form is predicted to be of lowest energy, which can partly be attributed to hydrogen bonding through the oximino nitrogen. In the nitro derivative, however, the preference to form a six membered ring owing to O–H–O hydrogen-bonded interactions makes the anti conformer (keto) the stablest. Further one of the nitrosophenol conformers of nitrolawsoneoxime turns out to be very close in energy (0.21 kJ mol^–1 higher) to this anti conformer. The consequences of hydrogen bonding on charge distribution and vibrational spectra are discussed.     

Ab initio and density functional theory based studies on collagen triplets

An understanding of the amino acid sequence dependent stability of polypeptides is of renowned interest to biophysicists and biochemists, in order to identify the nature of forces that stabilize the three-dimensional structure of proteins. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed. It is found from this study that proline can stabilize the collagen triplet only when other residues are also in the polyproline II conformation. Solvation studies of various triplets indicate that the presence of polar residues increases the free energy of solvation. Especially the triplets containing arginine residues displays a higher solvation free energy. The chemical hardness of all the triplets in collagen-like conformation has been found to be higher than that in the extended conformation. Studies on Gly–X–Y, Gly–X–Hyp, and Gly–Pro–Y triplets confirm that there will be local variations in the stability of collagen along the entire sequence.