Structural properties and isomerisation of simple S-nitrosothiols: ab initio studies with a simplified treatment of correlation effects
TL;DR: In this paper, the structure-stability relationship in S-Nitrosothiols (RSNOs) that govern their activity in vivo is not well understood, and useful structural information is provided.
Abstract: Despite the enormous biological significance, the structure-stability relationship in S-Nitrosothiols (RSNOs) that govern their activity in vivo is not well understood We provide useful structural
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TL;DR: It is suggested that RSNO reactions in vivo should be tightly controlled by the protein environment via modulation of the RSNO electronic structure through a 'ligand effect map' (LEM) approach.
Abstract: There is currently great interest in S-nitrosothiols (RSNOs) because formation of protein-based RSNOsprotein S-nitrosationhas been recently recognized as a major pathway of the biological function of nitric oxide, NO. Despite the growing number of S-nitrosated proteins identified in vivo, enzymatic processes that control reactions of biological RSNOs are still not well understood. In this article, we use a range of models to computationally demonstrate that specific interactions of RSNOs with charged and polar residues in proteins can result in dramatic modification of RSNO structure, stability, and reactivity. This unprecedented sensitivity of the −SNO group toward interactions with charged species is related to their unusual electronic structure that can be elegantly expressed in terms of antagonistic resonance structures. We propose a ‘ligand effect map’ (LEM) approach as an efficient way to estimate the environment effects on the −SNO groups in proteins without performing electronic structure calculations. Furthermore, the calculated ¹⁵N NMR signatures of these specific interactions suggest that ¹⁵N NMR spectroscopy can be an effective technique to identify and study these interactions experimentally. Overall, the results of this study suggest that RSNO reactions in vivo should be tightly controlled by the protein environment via modulation of the RSNO electronic structure.
6 citations
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TL;DR: In this article, the pairing matrix fluctuation was used to estimate the excitation energies of the N-electron system through particle-particle random phase approximation (pp-RPA) and particleparticle Tamm-Dancoff approximation(pp-TDA).
Abstract: Double, Rydberg, and charge transfer (CT) excitations have been great challenges for time-dependent density functional theory (TDDFT). Starting from an (N ± 2)-electron single-determinant reference, we investigate excitations for the N-electron system through the pairing matrix fluctuation, which contains information on two-electron addition/removal processes. We adopt the particle-particle random phase approximation (pp-RPA) and the particle-particle Tamm-Dancoff approximation (pp-TDA) to approximate the pairing matrix fluctuation and then determine excitation energies by the differences of two-electron addition/removal energies. This approach captures all types of interesting excitations: single and double excitations are described accurately, Rydberg excitations are in good agreement with experimental data and CT excitations display correct 1/R dependence. Furthermore, the pp-RPA and the pp-TDA have a computational cost similar to TDDFT and consequently are promising for practical calculations.
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TL;DR: In this paper, a detailed study of correlation effects in the oxygen atom was conducted, and it was shown that primitive basis sets of primitive Gaussian functions effectively and efficiently describe correlation effects.
Abstract: In the past, basis sets for use in correlated molecular calculations have largely been taken from single configuration calculations. Recently, Almlof, Taylor, and co‐workers have found that basis sets of natural orbitals derived from correlated atomic calculations (ANOs) provide an excellent description of molecular correlation effects. We report here a careful study of correlation effects in the oxygen atom, establishing that compact sets of primitive Gaussian functions effectively and efficiently describe correlation effects i f the exponents of the functions are optimized in atomic correlated calculations, although the primitive (s p) functions for describing correlation effects can be taken from atomic Hartree–Fock calculations i f the appropriate primitive set is used. Test calculations on oxygen‐containing molecules indicate that these primitive basis sets describe molecular correlation effects as well as the ANO sets of Almlof and Taylor. Guided by the calculations on oxygen, basis sets for use in correlated atomic and molecular calculations were developed for all of the first row atoms from boron through neon and for hydrogen. As in the oxygen atom calculations, it was found that the incremental energy lowerings due to the addition of correlating functions fall into distinct groups. This leads to the concept of c o r r e l a t i o n c o n s i s t e n t b a s i s s e t s, i.e., sets which include all functions in a given group as well as all functions in any higher groups. Correlation consistent sets are given for all of the atoms considered. The most accurate sets determined in this way, [5s4p3d2f1g], consistently yield 99% of the correlation energy obtained with the corresponding ANO sets, even though the latter contains 50% more primitive functions and twice as many primitive polarization functions. It is estimated that this set yields 94%–97% of the total (HF+1+2) correlation energy for the atoms neon through boron.
26,705 citations
TL;DR: A description of the ab initio quantum chemistry package GAMESS, which can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication.
Abstract: A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.
18,546 citations
TL;DR: Molpro (available at http://www.molpro.net) is a general-purpose quantum chemical program as discussed by the authors, which uses local approximations combined with explicit correlation treatments, highly accurate coupled-cluster calculations are now possible for molecules with up to approximately 100 atoms.
Abstract: Molpro (available at http://www.molpro.net) is a general-purpose quantum chemical program. The original focus was on high-accuracy wave function calculations for small molecules, but using local approximations combined with explicit correlation treatments, highly accurate coupled-cluster calculations are now possible for molecules with up to approximately 100 atoms. Recently, multireference correlation treatments were also made applicable to larger molecules. Furthermore, an efficient implementation of density functional theory is available.
2,999 citations
TL;DR: In this article, the second-order perturbation theory based on a CASSCF reference state is derived and implemented, where the first-order wave function includes the full space of interacting states and the zeroth-order Hamiltonian reduces to the MOller-Plesset Hamiltonian for a closed shell reference state.
Abstract: Second-order perturbation theory based on a CASSCF reference state is derived and implemented. The first-order wave function includes the full space of interacting states. Expressions for the contributions to the second-order energy are obtained in terms of up to four-particle density matrices for the CASSCF reference state. The zeroth-order Hamiltonian reduces to the MOller-Plesset Hamiltonian for a closed-shell reference state. The limit of the implementation is given by the number of active orbitals, which determines the size of the density matrices. It is presently around 13 orbitals. The method is illustrated in a series of calculations on H 2 , H 2 O, CH 2 , and F - , and the results are compared with corresponding full CI results
2,825 citations
TL;DR: It is argued that the ready availability of information pertaining to the applications and theoretical models can substantially increase the likelihood of novice users obtaining the desired accuracy from their calculations while simultaneously making better use of computer resources.
Abstract: A role for electronic structure databases in assisting users of quantum chemistry applications select better model parameters is discussed in light of experiences gained from a software prototype known as the Computational Chemistry Input Assistant (CCIA). It is argued that the ready availability of information pertaining to the applications and theoretical models can substantially increase the likelihood of novice users obtaining the desired accuracy from their calculations while simultaneously making better use of computer resources. Expert users, who find themselves contemplating studies in new areas of research, may also benefit from the proposed tools. For maximum impact, this assistance should be provided while users are actively engaged in preparing calculations. © 1996 by John Wiley & Sons, Inc.
2,149 citations