Regio- and stereo-chemical ring-opening reactions of the 2,3-epoxy alcohol derivative with nucleophiles: Explanation of the structures and C-2 selectivity supported by theoretical computations

The ring-opening reactions of (1aS,2S,6bR)-5-ethyl-2-hydroxyhexahydro-4H-oxireno[2,3-e]isoindole-4,6(5H)-dione were investigated under very mild and nonchelated conditions. C-2 selective ring-opening products were obtained with nucleophilic additions such as Cl-, Br- and N-3(-). The exact configuration of (3aS,4R,5R,6S,7aS)-5-chloro-2-ethyl-4,6-dihydroxyhexahydro-1H-isoindole-1,3(2H)-dione was determined by X-Ray diffraction analysis which was obtained from the reaction of epoxy alcohol with HCl . On the other hand, theoretical computations were carried out to explain the regioselectivity in the ring opening reaction of epoxy alcohols. The results showed that the ring-opening reaction of both epoxy alcohols proceeds in a kinetically controlled manner and regioselectivity occurs depending on the transition state. (c) 2022 Published by Elsevier B.V

2-alkilidensiklopenta-1, 3-diil biradikalerinin termal çevrimlerinin teorik çalışması.

Thermal rearrangements of Berson TMMs have been investigated. For this purpose, the potential energy surface of the singlet S state has been explored to test Benson’s Schemes 1-2 (Figure 1.10 and 1.11). It is verified that the enyne 9c plays a central role in connecting the two portions of the reaction path (Berson Schemes 1 and 2). Connectivity of successive minima on a given surface has been verified by intrinsic reaction coordinate (IRC) computations. Density functional theory (DFT) and multiconfiguration self consistent field (MCSCF) methods have been employed for these purposes. Further, single point coupled-cluster singles and doubles with perturbative triples (CCSD(T)) energy computations have been carried out at optimized DFT or MCSCF geometries. All transition states (TS) connecting each neighboring minimum have been located in the proposed mechanisms. It is concluded that the proposed mechanisms are confirmed by the theoretical calculations. The computed activation energy and enthalpy of reaction values are in good agreement with the available experimental values, only differing by a few kcal mol-1.Ph.D. - Doctoral Progra

Molint 1.0: An Application Programming Interface Framework for the Computation of Molecular Integrals and Their First Derivatives for the Density-Fitted Methods

The efficient computation of molecular integrals and their derivatives is a crucial step in molecular property evaluation in modern quantum chemistry. As an integral tensor decomposition technique, the density-fitting (DF) approach becomes a popular tool to reduce the memory and disk requirements for the electron repulsion integrals. In this study, an application programming interface (API) framework, denoted Molint (MFW), for the computation of molecular integrals and their first derivatives, over contracted Gaussian functions, for the density-fitted methods is reported. The MFW is free software and it includes overlap, dipole, kinetic, potential, metric, and 3-index integrals, and their first derivatives. Furthermore, the MFW provides a smooth approach to build the Fock matrix and evaluate analytic gradients for the density-fitted methods. The MFW is a C++/Fortran hybrid code, which can take advantage of shared-memory parallel programming techniques. Our results demonstrate that the MFW is an efficient and user-friendly API for the computation of molecular integrals and their first derivatives

Linear-Scaling Systematic Molecular Fragmentation Approach for High-Level Coupled-Cluster Methods: Coupled-Cluster Meets Macromolecules

The coupled-cluster (CC) singles and doubles with perturbative triples [CCSD(T)] method is frequently referred to as the “gold standard" of modern computational chemistry. However, the high computational cost of CCSD(T) [O(N7)], where N is the number of basis functions, limits its applications to small-sized chemical systems. To address this problem, efficient implementations of linear-scaling coupled-cluster methods, which employ the systematic molecular fragmentation (SMF) approach, are reported. In this study: (1) to achieve exact linear-scaling and to obtain a pure ab inito approach, we revise the handling of nonbonded interactions in the SMF approach (2) a new fragmentation algorithm, which yields smaller sized fragments; hence, better fits high-level CC methods is introduced (3) the new SMF approach is integrated with the high-level CC methods, denoted by LSSMF-CC, for the first time. Performances of the LSSMF-CC approaches, such as LSSMF-CCSD(T), are compared with their canonical versions for a set of alkane molecules, CnH2n+2 (n=6–10), which includes 142 molecules. Our results demonstrate that the LSSMF approach introduces negligible errors compared with the canonical methods, mean absolute errors (MAEs) are between 0.20–0.59 kcal mol-1 for LSSMF-CCSD(T). To further assess the accuracy of the LSSMF-CCSD(T) approach, we also consider several polyethylene (PE) models. For the PE set, the error of LSSMF-CCSD(T)/cc-pVDZ with respect to the experimental polymerization energies per unit are between 0.08–0.63 kcal/mol. To illustrate the efficiency and applicability of the LSSMF-CCSD(T) approach, we consider an alkane molecule with 10004 atoms. For this molecule, the LSSMF-CCSD(T)/cc-pVTZ energy computation on a Linux cluster with 100 nodes, 4 cores and 5 GB of memory are provided to each node, is performed just in ∼ 24 hours. As far as we know, this computation is an application of the CCSD(T) method on the largest chemical system to date. Overall, we conclude that (1) the LSSMF-CCSD(T) method can be reliably used for large scale chemical systems, where the canonical methods are not computationally affordable (2) the LSSMF-CCSD(T) method is very promising for accurate computation of energies in macromolecular systems (3) we believe that our study is a significant milestone in developing CC methods for large-scale chemical systems.</p

Energy and Analytic Gradients for the Orbital-Optimized Coupled-Cluster Doubles Method with the Density-Fitting Approximation: An Efficient Implementation

Efficient implementations of the orbital-optimized coupled-cluster doubles [or simply ``optimized CCD\u27\u27, OCCD, for short] method and its analytic energy gradients with the density-fitting (DF) approach, denoted by DF-OCCD, are presented. In addition to the DF approach, the Cholesky-decomposed variant (CD-OCCD) is also implemented for energy computations. The computational cost of the DF-OCCD method {(available in a plugin version of the {\sc DFOCC} module of {\sc Psi4})} is compared with that of the conventional OCCD {(from the {\sc Q-Chem} package)}. The OCCD computations were performed with the {\sc Q-chem} package, in which it is denoted by OD. In the conventional OCCD, one needs to perform four-index integrals transformations at each CCD iterations, which limits its applications to large chemical systems. Our results demonstrate that DF-OCCD provides dramatically lower computational costs compared to OCCD, there are almost 8-fold reductions in the computational time for the \ce{C6H14} molecule with the cc-pVTZ basis set. For open-shell geometries, interaction energies, and hydrogen transfer reactions, DF-OCCD provides significant improvements upon DF-CCD. {Further, the performance of the DF-OCCD method is substantially better for harmonic vibrational frequencies in the case of symmetry breaking problems. Moreover,} several factors make DF-OCCD more attractive compared to CCSD: (1) for DF-OCCD there is no need for orbital relaxation contributions in analytic gradient computations (2) active spaces can readily be incorporated into DF-OCCD (3) DF-OCCD provides accurate vibrational frequencies when symmetry-breaking problems are observed (4) in its response function, DF-OCCD avoids artificial poles; hence, excited-state molecular properties can be computed via linear response theory (5) Symmetric and asymmetric triples corrections based on DF-OCCD [DF-OCCD(T)] has a significantly better performance in near degeneracy regions

An adaptive large neighborhood search for an e-grocery delivery routing problem

Online shopping has become ever more indispensable to many people with busy schedules who have a growing need for services ranging for a wide variety of goods, which include standard (or “staple”) goods as well as “premium” goods, i.e. goods such as organic food, specialty gifts, etc. that offer higher value to consumers and higher profit margins to retailers. In this paper, we introduce a new mathematical programming formulation and present an efficient solution approach for planning the delivery services of online groceries to fulfill this diverse consumer demand without incurring additional inventory costs. We refer to our proposed model as the E-grocery Delivery Routing Problem (EDRP) as it generically represents a family of problems that an online grocery is likely to face. The EDRP is based on a distribution network where premium goods are acquired from a set of external vendors at multiple locations in the supply network and delivered to customers in a single visit. To solve this problem, we develop an improved Adaptive Large Neighborhood Search (ALNS) heuristic by introducing new removal, insertion, and vendor selection/allocation mechanisms. We validate the performance of the proposed ALNS heuristic through an extensive computational study using both the well-known Vehicle Routing Problem with Time Windows instances of Solomon and a set of new benchmark instances generated for the EDRP. The results suggest that the proposed solution methodology is effective in obtaining high quality solutions fast

Quadratically convergent algorithm for orbital optimization in the orbital-optimized coupled-cluster doubles method and in orbital-optimized second-order Møller-Plesset perturbation theory

© 2011 American Institute of Physics. The electronic version of this article is the complete one and can be found at: http://dx.doi.org/10.1063/1.3631129DOI: 10.1063/1.3631129Using a Lagrangian-based approach, we present a more elegant derivation of the equations necessary for the variational optimization of the molecular orbitals (MOs) for the coupled-cluster doubles (CCD) method and second-order Møller-Plesset perturbation theory (MP2). These orbital-optimized theories are referred to as OO-CCD and OO-MP2 (or simply “OD” and “OMP2” for short), respectively. We also present an improved algorithm for orbital optimization in these methods. Explicit equations for response density matrices, the MO gradient, and the MO Hessian are reported both in spin-orbital and closed-shell spin-adapted forms. The Newton-Raphson algorithm is used for the optimization procedure using the MO gradient and Hessian. Further, orbital stability analyses are also carried out at correlated levels. The OD and OMP2 approaches are compared with the standard MP2, CCD, CCSD, and CCSD(T) methods. All these methods are applied to H₂O, three diatomics, and the O₄⁺ molecule. Results demonstrate that the CCSD and OD methods give nearly identical results for H₂O and diatomics; however, in symmetry-breaking problems as exemplified by O₄⁺, the OD method provides better results for vibrational frequencies. The OD method has further advantagesover CCSD: its analytic gradients are easier to compute since there is no need to solve the coupledperturbed equations for the orbital response, the computation of one-electron properties are easier because there is no response contribution to the particle density matrices, the variational optimized orbitals can be readily extended to allow inactive orbitals, it avoids spurious second-order poles in its response function, and its transition dipole moments are gauge invariant. The OMP2 has these same advantages over canonical MP2, making it promising for excited state properties via linear response theory. The quadratically convergent orbital-optimization procedure converges quickly for OMP2, and provides molecular properties that are somewhat different than those of MP2 for most of the test cases considered (although they are similar for H₂O). Bond lengths are somewhat longer, and vibrational frequencies somewhat smaller, for OMP2 compared to MP2. In the difficult case of O₄⁺, results for several vibrational frequencies are significantly improved in going from MP2 to OMP2