Journal of Computational Chemistry

doi: 10.1002/jcc.25455pmid: N/A

doi: 10.1002/jcc.25458pmid: N/A

Mironov, Vladimir; Alexeev, Yuri; Mulligan, Vikram Khipple; Fedorov, Dmitri G.

doi: 10.1002/jcc.25589pmid: 30368851

The alanine dipeptide is a standard system to model dihedral angles in proteins. It is shown that obtaining the Ramachandran plot accurately is a hard problem because of many local minima; depending on the details of geometry optimizations, different Ramachandran plots can be obtained. To locate all energy minima, starting from geometries from MD simulations, 250,000 geometry optimizations were performed at the level of RHF/6‐31G*, followed by re‐optimizations of the located 827 minima at the level of MP2/6–311++G**, yielding 30 unique minima, most of which were not previously reported in literature. Both in vacuo and solvated structures are discussed. The minima are systematically categorized based on four backbone dihedral angles. The Gibbs energies are evaluated and the structural factors determining the relative stabilities of conformers are discussed. © 2018 Wiley Periodicals, Inc.

De Silva, Nuwan; Adreance, Matthew A.; Gordon, Mark S.

doi: 10.1002/jcc.25596pmid: 30368848

The Grimme‐D3 semi‐empirical dispersion energy correction has been implemented for the original effective fragment potential for water (EFP1), and for systems that contain water molecules described by both correlated ab initio quantum mechanical (QM) molecules and EFP1. Binding energies obtained with these EFP1‐D and QM/EFP1‐D methods were tested using 27 benchmark species, including neutral, protonated, deprotonated, and auto‐ionized water clusters and nine solute–water binary complexes. The EFP1‐D and QM/EFP1‐D binding energies are compared with those obtained using fully QM methods: second‐order perturbation theory, and coupled cluster theory, CCSD(T), at the complete basis set (CBS) limit. The results show that the EFP1‐D and QM/EFP1‐D binding energies are in good agreement with CCSD(T)/CBS binding energies with a mean absolute error of 5.9 kcal/mol for water clusters and 0.8 kcal/mol for solute–water binary complexes. © 2018 Wiley Periodicals, Inc.

Tachibana, Akitomo

doi: 10.1002/jcc.25600pmid: 30299560

Application of Alpha‐oscillator theory to quantum electrodynamics (QED) solves the mystery (Feynman) of the double‐slit phenomenon involved in the foundation of quantum mechanics (QM). Even if with the same initial condition given, different spots on the screen can be predicted deterministically with no introduction of hidden variables. The interference pattern is similar to, but cannot be reproduced quantitatively by, that of the QM wave function, contrary to many‐years‐anticipation: a new prediction, awaiting experimental test over and above the Bohr–Einstein gedanken experiment. The general proof has already been published in Ref. [3a] and the concrete numerical algorithm of the extended normal mode technique for concrete trajectory of one electron in Ref. [3b]. In this article, (1) the new “interpretation” of the QED wave function is given in section “Interpretation of Wave Function in QED”: the QED wave function used in the extended normal mode technique gives probability density distribution function of the initial values of trajectories. Moreover, (2) for the sake of demonstration of this new interpretation, the time‐independent stationary state QM wave function is substituted to the QED wave function in section “Internal Self‐Stress of Energetic Particles”: the QED wave function is realized by internal self‐stress revealed as energy density at the initial conditions. The renewed energy density is applied to study a unified scheme for generalized chemical reactivity. This is a new kind of chemical force acting in between electrons not in between nuclei. This paves a way for more advanced time‐dependent simulation of electronic structure and dynamics in chemical reaction dynamics by tracing trajectories of many electrons. © 2018 Wiley Periodicals, Inc.

Nandi, Apurba; Qu, Chen; Bowman, Joel M.

doi: 10.1002/jcc.25601pmid: 30284291

Diffusion Monte Carlo (DMC) simulations have been used to obtain quantum zero‐point energies of methanol and all its isotopologs and isotopomers, using a new, accurate semi‐global potential energy surface. This potential energy surface is a precise, permutationally invariant fit to 6676 ab initio energies, obtained at the CCSD(T)‐F12b/aug‐cc‐pVDZ level of theory. Quantum zero‐point energies of deuterated methanol isotopomers are very close to each other and so a simple statistical argument can be used to estimate the populations of each isotopomer at very low‐temperatures. The DMC simulations also indicate that there is virtually zero probability for H/D exchange in the zero‐point state. © 2019 Wiley Periodicals, Inc.

Kawakami, Takashi; Miyagawa, Koichi; Sharma, Sandeep; Saito, Toru; Shoji, Mitsuo; Yamada, Satoru; Yamanaka, Shusuke; Okumura, Mitsutaka; Nakajima, Takahito; Yamaguchi, Kizashi

doi: 10.1002/jcc.25602pmid: 30341945

Bernales, Varinia; Froese, Robert D.

doi: 10.1002/jcc.25605pmid: 30379334

DFT and CCSD(T) methods were used to examine 61 different rhodium catalysts for the hydroformylation of ethylene. The carbon monoxide (CO) stretching frequency was a key electronic parameter to understand the π‐accepting nature of the ligand. Normally, π‐accepting ligands lead to increased CO stretching frequencies and a reduction in CO dissociation energy. There was no relationship between CO dissociation energy and CO stretching frequency. However, a clear relationship exists between the ethylene insertion barrier (from the rhodium dicarbonyl hydride resting state) and the CO stretching frequency as stronger π‐accepting ligands systematically led to a reduction in the barrier. Due to the multistep nature of the rate‐limiting step, the overall barrier can be divided into the CO/ethylene equilibrium and an intrinsic ethylene insertion barrier and both are systematically reduced as the π‐accepting nature of the ligand is increased. A comparison of the carbonylation transition state (TS) to the ethylene insertion TS allowed us to understand reversibility of olefin insertion. While the ethylene insertion TS systematically decreases with increasing CO stretching frequency, the carbonylation TS is relatively flat. The lines cross at 2156 cm−1 implying a change in the rate‐limiting step in this region given a standard set of process conditions. © 2018 Wiley Periodicals, Inc.

Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori

doi: 10.1002/jcc.25606pmid: 30306615

Recent experiments concerning prebiotic materials syntheses suggest that the iron‐bearing meteorite impacts on ocean during Late Heavy Bombardment provided abundant organic compounds associated with biomolecules such as amino acids and nucleobases. However, the molecular mechanism of a series of chemical reactions to produce such compounds is not well understood. In this study, we simulate the shock compression state of a meteorite impact for a model system composed of CO2, H2O, and metallic iron slab by ab initio molecular dynamics combined with multiscale shock technique, and clarify possible elementary reaction processes up to production of organic compounds. The reactions included not only pathways similar to the Fischer–Tropsch process known as an important hydrocarbon synthesis in many planetary processes but also those resulting in production of a carboxylic acid. It is also found that bicarbonate ions formed from CO2 and H2O participated in some forms in most of these observed elementary reaction processes. These findings would deepen the understanding of the full range of chemical reactions that could occur in the meteorite impact events. © 2018 Wiley Periodicals, Inc.

Miyahara, Tomoo; Nakatsuji, Hiroshi

doi: 10.1002/jcc.25608pmid: 30351451

Three‐dimensional accurate potential energy surfaces around the local minima of NO2− and NO2 were calculated with the SAC/SAC‐CI analytical energy gradient method. Therefrom, the ionization photoelectron spectra of NO2−, the equilibrium geometries and adiabatic electron affinity of NO2, and the vibrational frequencies including harmonicity and anharmonicity of NO2− and NO2 were obtained. The calculated electron affinity was in reasonable agreement with the experimental value. The SAC‐CI photoelectron spectra of NO2− at 350 K and 700 K including the rotational effects were calculated using the Franck–Condon approximation. The theoretical spectra reproduced well the fine experimental photoelectron spectra observed by Ervin et al. (J. Phys. Chem. 1988, 92, 5405). The results showed that the ionizations from many vibrational excited states as well as the vibrational ground state are included in the experimental photoelectron spectra especially at 700 K and that the rotational effects are important to reproduce the experimental photoelectron spectra of both temperatures. The SAC/SAC‐CI theoretical results supported the analyses of the spectra by Ervin et al., except that we could show some small contributions from the asymmetric‐stretching mode of NO2−. © 2018 Wiley Periodicals, Inc.