Features of CPB: A Poisson–Boltzmann solver that uses an adaptive cartesian grid

The capabilities of an adaptive Cartesian grid (ACG)‐based Poisson–Boltzmann (PB) solver (CPB) are demonstrated. CPB solves various PB equations with an ACG, built from a hierarchical octree decomposition of the computational domain. This procedure decreases the number of points required, thereby reducing computational demands. Inside the molecule, CPB solves for the reaction‐field component (?_rf) of the electrostatic potential (?), eliminating the charge‐induced singularities in ?. CPB can also use a least‐squares reconstruction method to improve estimates of ? at the molecular surface. All surfaces, which include solvent excluded, Gaussians, and others, are created analytically, eliminating errors associated with triangulated surfaces. These features allow CPB to produce detailed surface maps of ? and compute polar solvation and binding free energies for large biomolecular assemblies, such as ribosomes and viruses, with reduced computational demands compared to other Poisson–Boltzmann equation solvers. The reader is referred to http://www.continuum‐dynamics.com/solution‐mm.html for how to obtain the CPB software. © 2014 Wiley Periodicals, Inc.     

FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations

Within molecular dynamics simulations of protein–solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifacts concerning structure and dynamics of the simulated systems. To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-adapted multipole method (SAMM) [C. Niedermeier and P. Tavan, J. Chem. Phys., 101 , 734 (1994)] with a multiple-time-step method. The computational effort for MD simulations required within our fast multiple-time-step structure-adapted multipole method (FAMUSAMM) scales linearly with the number of particles. For a system with 36,000 atoms we achieve a computational speed-up by a factor of 60 as compared with the exact evaluation of the Coulomb forces. Extended test simulations show that the applied approximations do not seriously affect structural or dynamical properties of the simulated systems. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1729–1749, 1997     

Electronic energy functionals: Levy–Lieb principle within the ground state path integral quantum Monte Carlo

We propose a theoretical/computational protocol based on the use of the Ground State Path Integral Quantum Monte Carlo for the calculation of the kinetic and Coulomb energy density for a system of N interacting electrons in an external potential. The idea is based on the derivation of the energy densities via the (N ? 1)‐conditional probability density within the framework of the Levy–Lieb constrained search principle. The consequences for the development of energy functionals within the context of density functional theory are discussed. We propose also the possibility of going beyond the energy densities and extend this idea to a computational procedure where the (N ? 1)‐conditional probability is an implicit functional of the electron density, independently from the external potential. In principle, such a procedure paves the way for an on‐the‐fly determination of the energy functional for any system. © 2012 Wiley Periodicals, Inc.     

Electronic Characterization of Vis–NIR Absorbing Noninnocent Ruthenium Oxyquinolate–merocyanine Complexes and their Photoacoustic Emission in Aqueous Micellar Solution†

The electronic and photophysical properties for a series of ruthenium(II) polypyridyl dyes are presented where a π-accepting 5-(vinyl-cyanine)-8-oxyquinolate class of ligand is incorporated to yield an improved vis–NIR absorption. A combination of computational, UV–vis–NIR absorption, phosphorescence emission and cyclic voltammetry studies are used to probe the influence of these ligands on complex electronic and photophysical properties. To assess their potential as vis–NIR photoacoustic contrast agents, select complexes were formulated in a PBS buffer/Tween® 20 solvent system. The p-quinolin-1-ium, 1,3,3-trimethyl-3H-indol-1-ium and 1,1,3-trimethyl-1H-benzo[e]indol-3-ium acceptor groups each impart a strong 680 nm optical absorption and photoacoustic emission on par with the performance exhibited by both the methylene blue and cryptocyanine commercial dyes.     

Assessment and acceleration of binding energy calculations for protein–ligand complexes by the fragment molecular orbital method

In the field of drug discovery, it is important to accurately predict the binding affinities between target proteins and drug applicant molecules. Many of the computational methods available for evaluating binding affinities have adopted molecular mechanics‐based force fields, although they cannot fully describe protein–ligand interactions. A noteworthy computational method in development involves large‐scale electronic structure calculations. Fragment molecular orbital (FMO) method, which is one of such large‐scale calculation techniques, is applied in this study for calculating the binding energies between proteins and ligands. By testing the effects of specific FMO calculation conditions (including fragmentation size, basis sets, electron correlation, exchange‐correlation functionals, and solvation effects) on the binding energies of the FK506‐binding protein and 10 ligand complex molecule, we have found that the standard FMO calculation condition, FMO2‐MP2/6‐31G(d), is suitable for evaluating the protein–ligand interactions. The correlation coefficient between the binding energies calculated with this FMO calculation condition and experimental values is determined to be R = 0.77. Based on these results, we also propose a practical scheme for predicting binding affinities by combining the FMO method with the quantitative structure–activity relationship (QSAR) model. The results of this combined method can be directly compared with experimental binding affinities. The FMO and QSAR combined scheme shows a higher correlation with experimental data (R = 0.91). Furthermore, we propose an acceleration scheme for the binding energy calculations using a multilayer FMO method focusing on the protein–ligand interaction distance. Our acceleration scheme, which uses FMO2‐HF/STO‐3G:MP2/6‐31G(d) at R_int = 7.0 Å, reduces computational costs, while maintaining accuracy in the evaluation of binding energy. © 2015 Wiley Periodicals, Inc.     

Conformationally Controlled sp3-Hydrocarbon-Based α-Helix Mimetics

With over 60 % of protein–protein interfaces featuring an α-helix, the use of α-helix mimetics as inhibitors of these interactions is a prevalent therapeutic strategy. However, methods to control the conformation of mimetics, thus enabling maximum efficacy, can be restrictive. Alternatively, conformation can be controlled through the introduction of destabilizing syn-pentane interactions. This tactic, which is often adopted by Nature, is not a common feature of lead optimization owing to the significant synthetic effort required. Through assembly-line synthesis with NMR and computational analysis, we have shown that alternating syn–anti configured contiguously substituted hydrocarbons, by avoiding syn-pentane interactions, adopt well-defined conformations that present functional groups in an arrangement that mimics the α-helix. The design of a p53 mimetic that binds to Mdm2 with moderate to good affinity, demonstrates the therapeutic promise of these scaffolds.     

Organocatalytic Asymmetric 1,6‐Addition/1,4‐Addition Sequence to 2,4‐Dienals for the Synthesis of Chiral Chromans

A novel asymmetric organocatalytic 1,6‐addition/1,4‐addition sequence to 2,4‐dienals is described. Based on a 1,6‐Friedel–Crafts/1,4‐oxa‐Michael cascade, the organocatalyst directs the reaction of hydroxyarenes with a vinylogous iminium‐ion intermediate to give only one out of four possible regioisomers, thus providing optically active chromans in high yields and 94–99 % ee. Furthermore, several transformations are presented, including the formation of an optically active macrocyclic lactam. Finally, the mechanism for the novel reaction is discussed based on computational studies.     

σ‐Noninnocence: Masked Phenyl‐Cation Transfer at Formal NiIV

Reductive elimination is an elementary organometallic reaction step involving a formal oxidation state change of ?2 at a transition‐metal center. For a series of formal high‐valent Ni^IV complexes, aryl–CF₃ bond‐forming reductive elimination was reported to occur readily (Bour et al. J. Am. Chem. Soc. 2015 , 137, 8034–8037). We report a computational analysis of this reaction and find that, unexpectedly, the formal Ni^IV centers are better described as approaching a +II oxidation state, originating from highly covalent metal–ligand bonds, a phenomenon attributable to σ‐noninnocence. A direct consequence is that the elimination of aryl–CF₃ products occurs in an essentially redox‐neutral fashion, as opposed to a reductive elimination. This is supported by an electron flow analysis which shows that an anionic CF₃ group is transferred to an electrophilic aryl group. The uncovered role of σ‐noninnocence in metal–ligand bonding, and of an essentially redox‐neutral elimination as an elementary organometallic reaction step, may constitute concepts of broad relevance to organometallic chemistry.     

Radical 4‐exo Cyclizations via Template Catalysis

The mechanism of catalytic 4‐exo cyclizations without gem‐dialkyl substitution was investigated by a comparison of cyclic voltammetry, EPR, and computational studies with previously published synthetic results. The most active catalyst is a super‐unsaturated 13‐electron titanocene(III) complex that is formed by supramolecular activation through hydrogen bonding. The template catalyst binds radicals via a two‐point binding that is mandatory for the success of the 4‐exo cyclization. The computational investigations revealed that formation of the observed trans‐cyclobutane product is not possible from the most stable substrate radical. Instead, the most stable product is formed with the lowest energy of activation from a disfavored substrate in a Curtin–Hammett related scenario.     

Usefulness of modified virtual orbitals in multireference CI procedure illustrated by calculations on lithium clusters

The maximization of the exchange interaction between the canonical Hartree–Fock virtual and occupied orbitals leads to a transformed set of virtual orbitals which are well suited as one-electron functions for CI calculations. The procedure, generally known for a long time is seldom applied, despite its simplicity and very low computational demand. However, it is found to be particularly useful in the case of multireference CI, since an improved energy is obtained with a considerable shortening of the CI expansion. Moreover, in the final CI wave function, several configurations appear with considerable weight, thus allowing an easy choice of additional configurations to be inserted in the definition of a new zero-order wave function. The efficiency of the computational procedure is discussed for the case of a Li₆ cluster of D_3h symmetry and for the NaCO and PdCO complexes. Results are reported for the relative stability of four different geometrical arrangements of the Li₆ cluster.     

Bond length alternation in cyclic polyenes. V. Local finite-order perturbation theory approach

The finite-order many-body perturbation theory using the localized Wannier orbital basis is applied to the problem of bond length alternation in the Pariser–Parr–Pople model of cyclic polyenes C_N H_N, N = 4v + 2, which may be regarded as a simplified model of polyacetylene. Both the Møller–Plesset and the Epstein–Nesbet-type partitionings of the model Hamiltonian are employed. The localized orbital basis enables an efficient truncation of the perturbation theory summations over the intermediate states as well as an elimination of energetically unimportant diagrams, thus enabling one to obtain the fourth-order Møller–Plesset-perturbation energies with a relatively small computational effort even for large polyenes. The results obtained with the second-, third-, and fourth-order Møller–Plesset and with the third-order Epstein–Nesbet perturbation theories yield very similar bond length distortions (about 0.05 Å) and stabilization energies per site (about 0.04 eV) as obtained earlier with the RHF , one-parameter AMO , and delocalized orbital perturbation theories. The effects of truncation and diagram elimination in the fourth-order Møller–Plesset perturbation theory and the abnormal behavior of the second-order Epstein–Nesbet perturbation theory results in the localized Wannier basis near the instability threshold of the RHF solutions are discussed.     

Unexpected Direct Synthesis of N‐Vinyl Amides through Vinyl Azide–Enolate [3+2] Cycloaddition

The unexpected synthesis of industrially important N ‐vinyl amides directly from aldehydes and α,β‐unsaturated N ‐vinyl amides from esters is reported. This reaction probably proceeds through an initial [3+2] azide–enolate cycloaddition involving a vinyl azide generated in situ. A survey of the reaction scope and preliminary mechanistic findings supported by quantum computational analysis are reported, with implications for the future development of atom‐efficient amide synthesis. Intriguingly, this study suggests that (cautious) reevaluation of azidoethene as a synthetic reagent may be warranted.     

Reactivity of a Nickel(II) Bis(amidate) Complex with meta‐Chloroperbenzoic Acid: Formation of a Potent Oxidizing Species

Herein, we report the formation of a highly reactive nickel–oxygen species that has been trapped following reaction of a Ni^II precursor bearing a macrocyclic bis(amidate) ligand with meta‐chloroperbenzoic acid (HmCPBA). This compound is only detectable at temperatures below 250 K and is much more reactive toward organic substrates (i.e., C?H bonds, C?C bonds, and sulfides) than previously reported well‐defined nickel–oxygen species. Remarkably, this species is formed by heterolytic O?O bond cleavage of a Ni–HmCPBA precursor, which is concluded from experimental and computational data. On the basis of spectroscopy and DFT calculations, this reactive species is proposed to be a Ni^III–oxyl compound.     

Heck反应中环钯化合物催化剂活化过程的理论研究

本文利用B3PW91 DFT方法对Heck反应中环钯化合物催化剂的活化过程进行了研究。我们考虑了两种可能的途径（1.阴离子还原开裂Pd-C键; 2.烯烃插入Pd-C键随后进行β-H消除）。研究结果表明，在反应条件下环钯化合物通过烯烃插入Pd-C键以及随后的β-H消除被活化。     

Large-scale RPA calculations of chiroptical properties of organic molecules: Program RPAC

The computational considerations involved in calculating ordinary and rotatory intensities and electronic excitation energies in the random phase approximation (RPA ) are examined. We employ a localized orbital formulation in order to analyze the results in terms of local and charge-transfer excitations. Occupied orbitals are localized by the Foster–Boys procedure. The virtual space is transformed into a localized “valence” set that maximizes dipole strengths with the occupied counterparts, and a delocalized remainder. The two-electron integral transformation is performed with an efficient algorithm, based on Diercksen's, that generates only the particle–hole-type integrals required in the RPA . The lowest solutions of the RPA equations are obtained iteratively using a modification of the Davidson-Liu simultaneous vector expansion method. This allows the inclusion of the entire set of particle–hole states supported by a basis set of up to 102 orbitals. Calculations at this level give better excitation energies and intensities than SDCI methods, at substantial savings in computational effort. Comparative timings, computed results and analysis in terms of localized orbitals are given for planar and distorted ethylene using extended atomic orbital bases including diffuse functions. The results for planar ethylene are in excellent agreement with experiment.     

Unexpected Direct Synthesis of N-Vinyl Amides through Vinyl Azide–Enolate [3+2] Cycloaddition

The unexpected synthesis of industrially important N-vinyl amides directly from aldehydes and α,β-unsaturated N-vinyl amides from esters is reported. This reaction probably proceeds through an initial [3+2] azide–enolate cycloaddition involving a vinyl azide generated in situ. A survey of the reaction scope and preliminary mechanistic findings supported by quantum computational analysis are reported, with implications for the future development of atom-efficient amide synthesis. Intriguingly, this study suggests that (cautious) reevaluation of azidoethene as a synthetic reagent may be warranted.     

Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integrator

A density matrix evolution method [H. J. C. Berendsen and J. Mavri, J. Phys. Chem., 97, 13464 (1993)] to simulate the dynamics of quantum systems embedded in a classical environment is applied to study the inelastic collisions of a classical particle with a five-level quantum harmonic oscillator. We improved the numerical performance by rewriting the Liouville–von Neumann equation in the interaction representation and so eliminated the frequencies of the unperturbed oscillator. Furthermore, replacement of the fixed time step fourth-order Runge–Kutta integrator with an adaptive step size control fourth-order Runge–Kutta resulted in significantly lower computational effort at the same desired accuracy. © 1996 by John Wiley & Sons, Inc.     

CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes

We have developed and implemented a new ab initio code, Ceres (Computational Emulator of Rare Earth Systems), completely written in C++11, which is dedicated to the efficient calculation of the electronic structure and magnetic properties of the crystal field states arising from the splitting of the ground state spin‐orbit multiplet in lanthanide complexes. The new code gains efficiency via an optimized implementation of a direct configurational averaged Hartree–Fock (CAHF) algorithm for the determination of 4f quasi‐atomic active orbitals common to all multi‐electron spin manifolds contributing to the ground spin‐orbit multiplet of the lanthanide ion. The new CAHF implementation is based on quasi‐Newton convergence acceleration techniques coupled to an efficient library for the direct evaluation of molecular integrals, and problem‐specific density matrix guess strategies. After describing the main features of the new code, we compare its efficiency with the current state–of–the–art ab initio strategy to determine crystal field levels and properties, and show that our methodology, as implemented in Ceres , represents a more time‐efficient computational strategy for the evaluation of the magnetic properties of lanthanide complexes, also allowing a full representation of non‐perturbative spin‐orbit coupling effects. © 2017 Wiley Periodicals, Inc.     

PICVib: An accurate,fast, and simple procedure to investigate selected vibrational modes at high theoretical levels

A new approach Procedure for Investigating Categories of Vibrations (PICVib) for estimating vibrational frequencies of selected modes using only the structure and energy calculations at a more demanding computational level is presented and explored. The PICVib has an excellent performance at only a small fraction of the computational demand required for a complete analytical calculation. The errors are smaller than ca. 0.5% when DFT functionals are combined with high level ab initio methods. The approach is general because it can use any quantum chemical program and electronic structure method. It is very robust because it was validated for a wide range of frequency values (ca. 20–4800 cm^–1) and systems: XH₃ (D_3h) with X = B, Al, Ga, N, P, As, O, S, and Se, YH₄ (D_4h) with Y = C, Si, and Ge, conformers of RDX, S_N2 and E2 reactions, [W(dppe)₂(NNC₅H₁₀)] complex, carbon nanotubes, and hydrogen‐bonded complexes including guanine‐cytosine pair. © 2012 Wiley Periodicals, Inc.