TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations

Summary We have developed a computer program with the necessary mathematical formalism for the geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially be sampled during typical molecular dynamics simulations. This formalism has been incorporated into TRAJELIX, a new module within the SIMULAID framework (http://inka.mssm.edu/~mezei/simulaid/) that is capable of monitoring distortions of alpha-helices in terms of their displacement, global and local tilting, rotation around their axes, compression/extension, winding/unwinding, and bending. Accurate evaluation of these global and local structural properties of the helix can help study possible intramolecular and intermolecular changes in the helix packing of alpha-helical membrane proteins, as shown here in an application to the interacting helical domains of rhodopsin dimers. Quantification of the dynamic structural behavior of alpha-helical membrane proteins is critical for our understanding of signal transduction, and may enable structure-based design of more specific and efficient drugs.     

T-shaped platinum boryl complexes: synthesis and structure

A series of cationic T-shaped 14-electron boryl complexes of the type trans-[(Cy(3)P)(2)Pt{B(X)X'}](+) (X=Br; X'=ortho-tolyl, tBu, NMe(2), piperidyl, Br; XX'=(NMe(2))(2), catecholato) were synthesized by halide abstraction from trans-[(Cy(3)P)(2)Pt(Br){B(X)X'}] (Cy=cyclohexyl) with Na[BAr(f) (4)] (Ar(f)=3,5-(CF(3))(2)C(6)H(3)), K[B(C(6)F(5))(4)], or Na[BPh(4)]. X-ray diffraction studies were performed on all compounds, revealing a subtle correlation between the trans-influence of the boryl moiety and the Pt--H and Pt--C separations. However, no notable agostic C--H interaction with the platinum center was detected. trans-[(Cy(3)P)(2)Pt(BCat)](+) (Cat=catecholato), the complex with the shortest Pt--H and Pt--C distances, was treated with Lewis bases (L), forming compounds of the type trans-[(Cy(3)P)(2)Pt(L)(BCat)](+), thus proving a decisive influence of the degree of trans-influence exerted by the boryl ligands on the chemical reactivity of the title complexes. Another point that was investigated and clarified is the different behavior of trans-[(Cy(3)P)(2)Pt(Br){B(Br)Mes}] (Mes=mesityl) towards K[B(C(6)F(5))(4)] with formation of the borylene species trans-[(Cy(3)P)(2)Pt(Br)(BMes)](+).     

Excited state tracking during the relaxation of coordination compounds

The ability to locate minima on electronic excited states (ESs) potential energy surfaces both in the case of bright and dark states is crucial for a full understanding of photochemical reactions. This task has become a standard practice for small- to medium-sized organic chromophores thanks to the constant developments in the field of computational photochemistry. However, this remains a very challenging effort when it comes to the optimization of ESs of transition metal complexes (TMCs), not only due to the presence of several electronic ESs close in energy, but also due to the complex nature of the ESs involved. In this article, we present a simple yet powerful method to follow an ES of interest during a structural optimization in the case of TMCs, based on the use of a compact hole-particle representation of the electronic transition, namely the natural transition orbitals (NTOs). State tracking using NTOs is unambiguously accomplished by computing the mono-electronic wave function overlap between consecutive steps of the optimization. Here, we demonstrate that this simple but robust procedure works not only in the case of the cytosine but also in the case of the ES optimization of a ruthenium nitrosyl complex which is very problematic with standard approaches. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Incoherent scattering of 59.54 keV gamma rays for some rare earth elements at low photon momentum transfers

Incoherent scattering functions S(x, Z) for six rare earth elements were evaluated from accurately measured whole atom differential incoherent scattering cross sections for 59.54 keV γ-rays scattered at 30°, 45°, 60° and 90° scattering angles corresponding to 1.24, 1.84, 2.40 and 3.39 Å⁻¹ photon momentum transfers. Our results for S(x, Z) are the first for these rare earth elements.     

Quantum-chemical estimates of geometric parameters of free radicals

Experimental geometries of the HCO^· and H₂CO^·+ -electron radicals were compared with those obtained from calculations with the total energy optimization carried out in the framework of widely used ab initio and semiempirical computational procedures. For each structural form of the radicals, the magnetic resonance parameters calculated in the MNDO approximation were correlated with experimental values determined by ESR spectroscopy. Comparative analysis of the results obtained indicates the possibility of systematic correction of the optimized geometric parameters of free radicals using the results of ESR measurements. A simple computational procedure for automatic geometry correction in the MNDO approximation is developed and evaluated.     

Development of spin‐orbit coupling for stochastic configuration interaction techniques

To perform spin‐orbit coupling calculations on atoms and molecules, good zeroth‐order wavefunctions are necessary. Here, we present the software development of the Monte Carlo Configuration Interaction (MCCI) method, to enable calculation of such properties, where MCCI iteratively constructs a multireference wavefunction using a stochastic procedure. In this initial work, we aim to establish the efficacy of this technique in predicting the splitting of otherwise degenerate energy levels on a range of atoms and small diatomic molecules. It is hoped that this work will subsequently act as a gateway toward using this method to investigate singlet‐triplet interactions in larger multireference molecules. We show that MCCI can generate very good results using highly compact wavefunctions compared to other techniques, with no prior knowledge of important orbitals. Higher‐order relativistic effects are neglected and spin‐orbit coupling effects are incorporated using first‐order degenerate perturbation theory with the Breit‐Pauli Hamiltonian and effective nuclear charges in the one‐electron operator. Results are obtained and presented for B, C, O, F, Si, S, and Cl atoms and OH, CN, NO, and C₂ diatomic radicals including spin‐orbit coupling constants and the relative splitting of the lowest energy degenerate state for each species. Convergence of MCCI to the full configuration interaction result is demonstrated on the multireference problem of stretched OH. We also present results from the singlet‐triplet interaction between the and both the and states of the O₂ molecule. © 2017 Wiley Periodicals, Inc.     

Size‐guided multi‐seed heuristic method for geometry optimization of clusters: Application to benzene clusters

Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size‐guided multi‐seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest‐energy configurations of the cluster with n − 1 molecules (seeds). The initial geometries are further optimized with the geometrical perturbations previously used for molecular clusters. These steps are repeated until the size n satisfies a predefined one. The method locates putative global minima of benzene clusters with up to 65 molecules. The performance of the method is discussed using the computational cost, rates to locate the global minima, and energies of initial geometries. © 2018 Wiley Periodicals, Inc.     

Preparation and Molecular Structure of Binuclear Nickel (I) Complex Bridged by 1,2,4, 5‐Benzenetetracarboxylato Tetravalent Anion

The title complex [(H₂O)₂(IMI)₃Ni(TCB)Ni(IMI)₃‐(H₂O)₂] H₂O (TCB = 1,2,4,5‐benzenetetracarboxylato te‐travalent anion; IMI = imidazole) has been prepared by the reaction of Ni(IMI)₃(Ac)₂ and TCB in aqueous solution. The crystal structure has been determined by single‐crystal X‐ray diffraction method. It crystallizes in the monoclinic system, space group P2₁/c(# 14), a = 1.2714(4) nm, b = 0.9411 (3) nm, c = 1.5869(4) nm, β= 108.54(2)°, V= 1.8001(9) nm³, Z = 2. The main feature of the crystal structure is a symmetric binuclear unit made up of two slightly distorted coordination octahedrons, which are bridged by TCB in monodentate fashion to each metal ion. Moreover three nitrogen atoms from three imidazoles, three oxygen atoms from two water molecules and one carboxylate group of TCB coordinated to a nickel (I) ion are found on a face of the octahedron respectively, so the octahedron is a facial isomer.     

N-苄叉基-1-氨基-萘及其类似物的构象与分子扭曲的共轭 驱动力

确定了N-[(4-二甲基氨基)-苄叉基]-2-氨基苯并咪唑(1)，N-[(4-二甲基氨基)-苄叉基]-2-氨基苯并噻唑(2)和N-苄叉基-1-氨基-萘(3)的晶体结构。利用AM1，RHF，DFT方法和STO-3G,4-31G,6-311G及6-311G基组，优化每个分子的23个扭曲构象(θ=0°～-89°)。尽管不同方法得到的最优构象的扭角不同，分子扭曲的驱动力总是起因于电子作用，在任一分子、任何电子态中，离域的π体系总是失稳定的，全平面构象不是π体系最稳定的构象。π电子的离域是分子扭曲的驱动力之一，与经典观点相反，非键原子间的核排斥作用是分子扭曲的阻力，而不是动力。