Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method

The first derivative of the total energy with respect to nuclear coordinates (the energy gradient) in the fragment molecular orbital (FMO) method is applied to second order M?ller-Plesset perturbation theory (MP2), resulting in the analytic derivative of the correlation energy in the external self-consistent electrostatic field. The completely analytic energy gradient equations are formulated at the FMO-MP2 level. Both for molecular clusters (H(2)O)(64) and a system with fragmentation across covalent bonds, a capped alanine decamer, the analytic FMO-MP2 energy gradients with the electrostatic dimer approximation are shown to be complete and accurate by comparing them with the corresponding numeric gradients. The developed gradient is parallelized with the parallel efficiency of about 97% on 32 Pentium4 nodes connected by Gigabit Ethernet.     

Adsorption of several gases on flexible metal organic framework [Cu(dhbc)2(4,4'-bpy)]·H2O

The adsorption of ten gases on the flexible metal organic framework material [Cu(dhbc)(2)(4,4'-bpy)]·H(2)O (Cu(db)) has been measured over a wide range of temperatures and pressures. The gate opening condition and driving force behind gate adsorption for Cu(db) were discussed by examining the adsorption isotherms. The adsorption isotherms for each adsorbate can be generalized to a characteristic curve using the adsorption potential energy (ε) and the adsorption volume. The adsorption potential (ε(gate)) at gate opening is almost constant over a wide range of temperatures; thus, the gate pressure at a desired temperature can be deduced using the ε(gate) evaluated from one adsorption isotherm. The gate opening capacity of the gases was arranged in the order: CO(2)≒N(2)O>C(2)H(4)≒Xe>CH(4)>CO>O(2)>Ar≒N(2)>H(2), which is governed by the interaction energy between the outer surface of Cu(db) and the adsorbate. It is suggested that the gate effect is brought about when the integral interaction energy of adsorbates with the Cu(db) surface exceeds a defined limit correlating with the π-π stacking energy of Cu(db) layers.     

A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin

The gradient for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFP), denoted by FMO∕EFP, was developed and applied to polypeptides solvated in water. The structures of neutral and zwitterionic tetraglycine immersed in water layers of 2.0, 2.5, 3.0, 3.5, 4.0, and 4.5 A? are investigated by performing FMO∕EFP geometry optimizations at the RHF∕cc-pVDZ level of theory for the solutes. The geometries optimized with FMO-RHF∕EFP are compared to those from the conventional RHF∕EFP and are found to be in very close agreement. Using the optimized geometries, the stability of the hydrated zwitterionic and neutral structures is discussed structurally and in terms of energetics at the second-order M?ller-Plesset theory (MP2)∕cc-pVDZ level. To demonstrate the potential of the method for proteins, the geometry of hydrated chignolin (protein data bank ID: 1UAO) was optimized, and the importance of the inclusion of water was examined by comparing the solvated and gas phase structures of chignolin with the experimental NMR structure.     

Transformation of ionic liquid into carbon nanotubes in confined nanospace

We have developed a two-step filling process for the nano-reaction of ionic liquid in a tip-closed SWNT, where fullerenes are inserted at the end of the host SWNT as a plug to prevent the leakage of the confined ionic liquid during heat treatment.     

Activation of a water molecule under mild conditions by ruthenacyclopentatriene: mechanism of hydrative cyclization of diynes

A ruthenium cyclic biscarbene complex reacted with a H(2)O molecule under mild conditions to produce η(5)-oxapentadienyl complex, that proved to be the intermediate in the catalytic hydrative cyclization of a diyne.     

Conjugate addition of copper(I) aldimines to α,β-unsaturated carbonyl compounds — synthesis of 1,4-diketones

This paper describes the finding that BF₃ etherate effectuates the conjugate additions of copper(I) aldimines, generated in situ from lithium aldimines and Cu(I) halide, to α,β-unsaturated carbonyl compounds to produce 4-(N-alkylimino)-ketones, which give on acid hydrolysis 1,4-diketone derivatives.     

Ring-transformation equilibrium with participation of π-bonded S in an isothiazole system. Synthesis of non-ring-transformed 5-(2-aminovinyl)isothiazole derivative via 1,3-silyl group shift

Substituents at 5-position of 5-amino-3-methyl- and 3-p-chlorophenyl-5-methylisothiazoles (7 and 8) were silylated and then lithiated to couple with aromatic nitriles in order to afford the adducts (4 and 5) via 1,3-silyl group shift. Desilylation of 5 with TBAF gave solely non-ring-transformed product (3-α-form). By using the pure sample of 3-α-form, the reversible ring-trans- formation (bond switch) was observed $\text{under neutral conditions}$ for the first time.