Ground states of molecules. XXV. MINDO/3. Improved version of the MINDO semiempirical SCF-MO method

Bingham, Richard C.; Dewar, Michael J. S.; Lo, Donald H.

doi:10.1021/ja00839a001

Cited by 1,680 publications

(211 citation statements)

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“…The accurate and fast calculation of forces is important in the description of reactions of energetic materials. This implementation described in this report uses MINDO3, a semi-empirical quantum mechanical method chosen here for its simplicity and speed [27,28,29]. More accurate density functional methods can be used instead, but this is not available in the current implementation.…”

Section: Chapter 2 Methodsmentioning

confidence: 99%

The potential, limitations, and challenges of divide and conquer quantum electronic structure calculations on energetic materials.

Tucker¹,

Magyar²

2012

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High explosives are an important class of energetic materials used in many weapons applications. Even with modern computers, the simulation of the dynamic chemical reactions and energy release is exceedingly challenging. While the scale of the detonation process may be macroscopic, the dynamic bond breaking responsible for the explosive release of energy is fundamentally quantum mechanical. Thus, any method that does not adequately describe bonding is destined to lack predictive capability on some level. Performing quantum mechanics calculations on systems with more than dozens of atoms is a gargantuan task, and severe approximation schemes must be employed in practical calculations. We have developed and tested a divide and conquer (DnC) scheme to obtain total energies, forces, and harmonic frequencies within semi-empirical quantum mechanics. The method is intended as an approximate but faster solution to the full problem and is possible due to the sparsity of the density matrix in many applications. The resulting total energy calculation scales linearly as the number of subsystems, and the method provides a path-forward to quantum mechanical simulations of millions of atoms. 3This page intentionally left blank.4

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Section: Chapter 2 Methodsmentioning

confidence: 99%

The potential, limitations, and challenges of divide and conquer quantum electronic structure calculations on energetic materials.

Tucker¹,

Magyar²

2012

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“…The "lens" for this "computer microscope" will be the modified-intermediate-neglect-of-differential-overlap (MINDO/3) molecular orbital (MO) method (22). This method has proved useful in studying many systems (22), including the structure of #-lactams (17,23). However, the method must be used with discretion because for certain systems this "lens" can cause distortions or aberrations in the picture seen (see references cited in ref.…”

Section: Methodsmentioning

confidence: 99%

“…Quantum mechanical computer calculations for "observing" TSs have the advantage of being able to stop the reaction at any point along the reaction path in order to observe at length species which, experimentally, would be very shortlived and not isolable. The "lens" for this "computer microscope" will be the modified-intermediate-neglect-of-differential-overlap (MINDO/3) molecular orbital (MO) method (22). This method has proved useful in studying many systems (22), including the structure of #-lactams (17,23).…”

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confidence: 99%

Transition state structures of a dipeptide related to the mode of action of beta-lactam antibiotics.

Boyd¹

1977

Proc. Natl. Acad. Sci. U.S.A.

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The tetrahedral adducts formed during nucleophilic attack by a hydroxyl ion on the carbonyl carbon of a model dipeptide, glycylglycine, were studied by modifiedintermediate-neglect-of-differential-overlap molecular orbital calculations. This dipeptide is taken to represent the D-alanyl-D-alanine terminus of the polypeptides involved in the crosslinking transpeptidation reaction of peptidoglycan in bacterial cell walls. It Twelve years ago it was proposed (1) that the fl-lactam antibiotics derive their antibacterial activity because their structure mimics that of a transition state (TS) species formed when a D-alanyl-D-alanine peptide bond is cleaved at the receptor site of a proteolytic enzyme in bacterial cell walls. This idea has remained viable in the light of most subsequent research (e.g., see refs. 2-7 and references cited therein). The final step in cell wall synthesis, the crosslinking of the peptidoglycan strands via a transpeptidation reaction, is the one that is upset by penicillins and cephalosporins. Depending on the organism and the antibiotic, the inhibition can involve a transpeptidase or a carboxypeptidase, be reversible or irreversible, and lead either directly or indirectly to death of growing bacteria (2,4,(8)(9)(10)(11)(12)(13)(14)(15)(16). In bacteria that have been studied (2), the peptidoglycan crosslinks are polypeptides which in their precursor form have. a D-alanyl-D-alanine terminus. Little is known about the structural details of the TSs through which this dipeptide passes. Tipper and Strominger (1) and later Lee (3) noted that a twisting about the peptide C-N bond from the usual trans planar arrangement produces a structure that is more analogous to that of the fl-lactam antibiotics. Because of their bicyclic ring systems, the antibiotics have a CC-NC dihedral angle (corresponding to the CaC'-NCa dehedral angle in a polypeptide) in the range 132°-157°(17). Calculations (3, 5) on the amount of energy this twisting from 1800 requires have shown such structures to be accessible with the energy derivable from the usual sorts of substrate-receptor interactions.In principle, information about the TS structure could be deduced from the three-dimensional arrangement of the functionalities in the receptor site(s) of the relevant enzymes.The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 METHODThe approach was to use the computer as a reaction vessel in which to observe the reactants coming together and starting to react. Quantum mechanical computer calculations for "observing" TSs have the advantage of being able to stop the reaction at any point along the reaction path in order to observe at length species which, experimentally, would be very shortlived and not isolable. The "lens" for this "computer microscope" will be the modified-intermediate-neglect-of-differential-overlap (MINDO/3) molecular orbital (MO) method (22). This method has ...

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“…Cálculos MINDO/3 -Cálculos MINDO/3 (do inglês Modified Intermediate Neglect of Differential Overlap, Negligência Intermediária Modificada do Recobrimento Diferencial) são cálculos de orbital molecular (MO) semi-empíricos 11 .…”

Section: Cálculos De Perturbação De Energiaunclassified

Glossário de termos usados no planejamento de fármacos (recomendações da IUPAC para 1997)

Sant’Anna¹

2002

Quím. Nova

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a N.T.: Por se tratar de um campo de evolução muito rápida, muitos termos novos surgiram desde a publicação do glossário em língua inglesa e a atual tradução. Este trabalho deve ser considerado como um esforço inicial para suprir as necessidades de padronização dos termos do planejamento computacional de fármacos na língua portuguesa, os quais já são usados com freqüência em artigos de química medicinal publicados em nosso país. b N.T.: AMBER também refere-se ao campo de força. Apesar deste campo de força ter sido parametrizado e definido para proteínas e ácidos nucléicos, parâmetros têm sido adicionados para estendê-lo para cálculos de outras classes de moléculas. c N.T.: Na maior parte dos casos as relações quantitativas envolvem atividades farmacológicas, mas o método pode ser aplicado igualmente a conjuntos de moléculas planejadas para causar qualquer ação sobre organismos vivos, inclusive tóxica, como é o caso dos pesticidas. d N.T.: O método CoMFA também pode ser usado para a análise de relações quantitativas entre afinidades (por receptores, etc.) com propriedades físico-químicas tridimensionais.

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Ground states of molecules. XXV. MINDO/3. Improved version of the MINDO semiempirical SCF-MO method

Cited by 1,680 publications

References 5 publications

The potential, limitations, and challenges of divide and conquer quantum electronic structure calculations on energetic materials.

The potential, limitations, and challenges of divide and conquer quantum electronic structure calculations on energetic materials.

Transition state structures of a dipeptide related to the mode of action of beta-lactam antibiotics.

Glossário de termos usados no planejamento de fármacos (recomendações da IUPAC para 1997)

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