β-Sheet Preferences from First Principles

Rossmeisl, Jan; Kristensen, Iben S.; Gregersen, Misha Marie; Jacobsen, Karsten Wedel; Nørskov, Jens K.

doi:10.1021/ja0359658

Cited by 24 publications

(20 citation statements)

References 27 publications

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“…Biological applications have focused principally on the modeling of enzymatic catalysis and active-site chemistry (79)(80)(81)(82)(83)(84)(85)(86)(87)(88), although interesting investigations of other phenomena, such as cooperativity in backbone hydrogen bonding (89) and modeling of ␤-sheet formation propensities by a periodic DFT calculation (90), have been performed recently. The use of QM͞MM methods permits incorporation of the full protein environment, which is crucial in an important subset of cases, as has recently been shown in cytochrome P450 (79), for example.…”

Section: Applicationsmentioning

confidence: 99%

Ab initioquantum chemistry: Methodology and applications

Friesner

2005

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

304

230

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This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller-Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical͞molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly.coupled cluster ͉ density functional theory ͉ second-order Modler-Plesser perturbation theory ͉ mixed quantum͞molecular mechanics O ver the past three decades, ab initio quantum chemistry has become an essential tool in the study of atoms and molecules and, increasingly, in modeling complex systems such as those arising in biology and materials science. The underlying core technology is computational solution of the electronic Schrodinger equation; given the positions of a collection of atomic nuclei, and the total number of electrons in the system, calculate the electronic energy, electron density, and other properties by means of a well defined, automated approximation (a ''model chemistry''). The ability to obtain ''goodenough'' solutions to the electronic Schrodinger equation for systems containing tens, or even hundreds, of atoms has revolutionized the ability of theoretical chemistry to address important problems in a wide range of disciplines; the Nobel Prize awarded to John Pople and Walter Kohn in 1998 is a reflection of this observation.In its exact form, the electronic Schrodinger equation is a many-body problem, whose computational complexity grows exponentially with the number of electrons, and hence, a brute force solution is intractable. Hartree-Fock theory, a mean field approach, produces reasonable results for many properties but is incapable of providing a robust description of reactive chemical events in which electron correlation has a major role. Thus, a key problem has been the development of treatments of electron correlation that exhibit a tractable scaling in computational effort with the size of the system. The considerable progress that has been made along these lines is outlined below.Given a well defined theoretical framework of approximation, the next requirement is efficient computational implementation. Considerable sophistication is required to achieve acceptable accuracy and efficiency; the leading quantum chemistry programs are millions of lines of computer code, and mathematical algorithms to reduce formal scaling of computational effort with system size have an increasingly crucial role in meeting the challenge of handling complex system relevant to practical applications. Below, the most important comp...

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Section: Applicationsmentioning

confidence: 99%

Ab initioquantum chemistry: Methodology and applications

Friesner

2005

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

304

230

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“…To probe the (non)-locality of the formation of the clusters in rotational space, we modelled hydrogen bonds between backbone peptide units by Density Function Theory (DFT), which has proven to be successful in describing basic secondary structure motifs 18,19 . We first probe the energy landscape of rotational space by modelling two peptide units as described under Methods.…”

Section: Article Nature Communications | Doi: 101038/ncomms6803mentioning

confidence: 99%

“…Exchange-correlation effects were described using the Perdew-Burke-Ernzerhof (PBE) functional. This functional has been proven successful in describing the hydrogen binding within, for example, helical polypeptides (including the transitions from the alpha-helix to the pi-and 3-10 helices) 18 and in describing the side-group propensities within beta-sheets 19 .…”

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confidence: 99%

Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

et al. 2014

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Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each C a effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment.

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“…Also, SCF convergence can be facilitated by applying Fermi smearing when calculating light-element cluster models composed of H, C, N, and O only: a few examples are defects in nanodiamond [31], cold-plasma methanol conversion [32], and amino acid adsorption on short single-walled carbon nanotubes (SWNTs) [33]. The use of periodic models along with electron smearing was reported for such diverse systems as platinum group metals with adsorbed species and dopants [34][35][36][37][38][39][40][41][42], from atoms to rather complex molecules adsorbed on other transition metals [43][44][45][46][47], sorption and catalysis on inorganic oxides [48][49][50][51][52][53] and other inorganic structures [54,55], to calculate structural and electronic properties of bulk and low-dimensional materials [56][57][58][59][60][61][62] (including SWNTs [56]), as well as to study peptide conformations [63]. Of particular interest for our research group are the recent works on carbon, silicon and germanium functionalization with carbene, silylene, germylene, and nitrene [64], noncovalent graphene functionalization with tetracyanoethylene [65] and hydrogen storage on lithium [66] and europium-doped [67] SWNTs.…”

Section: Introductionmentioning

confidence: 99%

“…There is a number of molecular modeling packages, in which electron smearing option is available: the reports cited above used the Amsterdam Density Functional (ADF) software [1,29]; Cerius2 [3], DMol 3 [4-28, 30-33, 35-37, 39, 42, 46, 47, 49, 53, 55, 58, 59, 61, 64, 66, 67] and Cambridge Sequential Total Energy Package (CASTEP) [45,60] modules (from Accelrys Inc., formerly Molecular Simulations Inc.); the Vienna Ab initio Simulation Package (VASP) [34, 38, 41, 43, 44, 50-52, 54, 65] CRYSTAL03 periodic code [40]; the plane-wave self-consistent field (PWscf) code [48,56]; the Quantum ESPRESSO package [57,62]; and the plane wave, pseudopotential code Dacapo [63].…”

Section: Introductionmentioning

confidence: 99%

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

Basiuk

2011

Int J of Quantum Chemistry

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To address the choice of an appropriate value of electron smearing to facilitate self-consistent field (SCF) convergence, we studied the interaction of doxorubicin with short armchair and zigzag single-walled carbon nanotube models with closed caps, at the PWC/DNP level of density functional theory. By gradually reducing the electron smearing value from a large and most commonly used one of 0.005 Ha to zero (Fermi occupation), we monitored the changes in close contacts between the interacting species, total energy of the molecular system, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy and isosurfaces, HOMO-LUMO gap energy, and plots of electrostatic potential. It became evident that the commonly used smearing values of !0.001 Ha can alter the results significantly (for example, by one order of magnitude for HOMO-LUMO gap energy). We suggest the setting of electron smearing value at 0.0001 Ha, which does not imply too high computation cost and can guarantee the results close to the ones obtained with Fermi occupation.

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β-Sheet Preferences from First Principles

Cited by 24 publications

References 27 publications

Ab initioquantum chemistry: Methodology and applications

Ab initioquantum chemistry: Methodology and applications

Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

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