Accurate Thermochemistry for Large Molecules with Modern Density Functionals

2014 ◽  
pp. 1-23 ◽  
Author(s):  
Marc Steinmetz ◽  
Andreas Hansen ◽  
Stephan Ehrlich ◽  
Tobias Risthaus ◽  
Stefan Grimme
Keyword(s):  
Density Functionals ◽  
Large Molecules

The low-resolution 3D-structure of porin, a channel-forming protein in E. coliouter membranes

1983 ◽  
Vol 41 ◽  
pp. 440-441
Author(s):  
A. Engel ◽  
D.L. Dorset ◽  
A. Massalski ◽  
J.P. Rosenbusch
Keyword(s):  
Crystal Packing ◽  
3D Structure ◽  
Gram Negative Bacteria ◽  
Protein Ratio ◽  
Crystal Forms ◽  
Large Molecules ◽  
Functional Studies ◽  
Voltage Dependent ◽  
Planar Membranes ◽  
Hexagonal Arrays

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.

Density functionals and chemical bond, diatomic molecules

1989 ◽  
Vol 86 ◽  
pp. 853-859 ◽  
Author(s):  
Federico Moscardó ◽  
José Pérez-Jordá ◽  
Emilio San-Fabián
Keyword(s):  
Chemical Bond ◽  
Diatomic Molecules ◽  
Density Functionals

HES 200/0.5 Is not HES 200/0.5

1995 ◽  
Vol 74 (06) ◽  
pp. 1452-1456 ◽  
Author(s):  
Johannes Treib ◽  
Anton Haass ◽  
Gerhard Pindur ◽  
Ulrich T Seyfert ◽  
Wolfgang Treib ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Hydroxyethyl Starch ◽  
Clinical Relevance ◽  
Dilution Effect ◽  
Repeated Administration ◽  
Plasma Viscosity ◽  
Degree Of Substitution ◽  
Pronounced Increase ◽  
Large Molecules ◽  
Mean Molecular Weight

SummaryThe plasma clearance of hydroxyethyl starch (HES) depends on the initial molecular weight and the degree of substitution. So far, little attention has been paid to the clinical relevance of the C2/C6 substitution ratio of hydroxyethyl starch.10 patients with cerebrovascular circulatory disturbance received hemodilution therapy for 10 days, consisting of 10% HES 200/0.5 (mean molecular weight 200 kD, degree of substitution 0.5) with a C2/C6 ratio of 13.4. A second group of 10 patients received a starch solution with identical initial molecular weight and degree of substitution but with a C2/C6 ratio of 5.7.After the administration of a single dose, no significant differences between the two groups were observed. After repeated administration, significant differences could be detected in hemorheology, coagulation and elimination (p<0.01). The larger C2/C6 ratio led to a higher intravascular mean molecular weight (95 vs. 84 kD), which in turn led to a higher increase in serum concentration during the therapy (14.7 vs.8.6 mg/ml). Hematocrit was lowered more (-30,5 vs. -23,5%) and plasma viscosity was increased more. There was also a more pronounced increase in partial thromboplastin time (+30% vs. +13%) and a factor of 2 larger decrease of factor VIII/von Willebrand factor-complex (p <0.01), which exceeded the dilution effect.The higher C2/C6 ratio of HES 200/0.5/13.4 slows down enzymatic degradation. After repeated administration of this starch, large molecules accumulate which are inefficiently degraded. The same effect has been observed after therapy with highly-substituted HES. This accumulation of large molecules leads to a beneficial longer lasting volume effect. The disadvantages include an increase in plasma viscosity and coagulation disturbances, which cannot be explained with the respective dilution effect alone. For these reasons, the C2/C6 ratio is of clinical relevance and should be included in the product labeling in the future.

A Multi-Layer Approach to the Equation of Motion Coupled-Cluster Method for the Electron Affinity

2020 ◽  
Author(s):  
Soumi Haldar ◽  
Achintya Kumar Dutta
Keyword(s):  
Electron Affinity ◽  
Electron Attachment ◽  
Equation Of Motion ◽  
Cluster Method ◽  
Coupled Cluster ◽  
Coupled Cluster Method ◽  
Large Molecules ◽  
Layer Method ◽  
Speed Up ◽  
Attachment Process

We have presented a multi-layer implementation of the equation of motion coupled-cluster method for the electron affinity, based on local and pair natural orbitals. The method gives consistent accuracy for both localized and delocalized anionic states. It results in many fold speedup in computational timing as compared to the canonical and DLPNO based implementation of the EA-EOM-CCSD method. We have also developed an explicit fragment-based approach which can lead to even higher speed-up with little loss in accuracy. The multi-layer method can be used to treat the environmental effect of both bonded and non-bonded nature on the electron attachment process in large molecules.<br>

CLB18: A New Structural Database with Unusual Carbon–Carbon Long Bonds

2020 ◽  
Author(s):  
Pierpaolo Morgante ◽  
Roberto Peverati
Keyword(s):  
Transition Metal Complexes ◽  
Low Cost ◽  
Geometry Optimization ◽  
Structure Calculation ◽  
Unique Property ◽  
Spin States ◽  
Calculation Methods ◽  
Large Molecules ◽  
Barrier Heights ◽  
Structural Database

<div><div><div><p>In this Letter, we introduce a new database called carbon long bond 18 (CLB18), composed of 18 structures with one long C–C bond. We use this new database to evaluate the performance of several low-cost methods commonly used for geometry optimization of medium and large molecules. We found that the long bonds in CLB18 are electronically different from those found in barrier heights databases. We also report the unexpected correlation between the results of CLB18 and those of the energetics of spin states in transition-metal complexes. Given this unique property, CLB18 can be a useful tool for assessing existing electronic structure calculation methods and developing new ones.</p></div></div></div>

PubChem and ChEMBL Beyond Lipinski

2019 ◽  
Author(s):  
Jean-Louis Reymond ◽  
Mahendra Awale ◽  
Daniel Probst ◽  
Alice Capecchi
Keyword(s):  
Nearest Neighbor ◽  
Molecular Shape ◽  
Biological Properties ◽  
Web Based ◽  
Large Molecules ◽  
Interactive Tools ◽  
Small Molecule Drugs ◽  
Pubchem Database ◽  
Nearest Neighbor Searches ◽  
Insight Into

<p>Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.</p>

A New Approach to Vibrational Analysis of Large Molecules by Density Functional Theory:  Wavenumber-Linear Scaling Method†

2002 ◽  
Vol 106 (14) ◽  
pp. 3580-3586 ◽  
Author(s):  
Hiroshi Yoshida ◽  
Kumi Takeda ◽  
Junko Okamura ◽  
Akito Ehara ◽  
Hiroatsu Matsuura
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Vibrational Analysis ◽  
Linear Scaling ◽  
Scaling Method ◽  
Functional Theory ◽  
New Approach ◽  
Large Molecules

Hydride Affinities for Main-Group Hydride Reductants: Assessment of Density Functionals and Trends in Reactivities

2021 ◽  
Vol 125 (3) ◽  
pp. 835-842
Author(s):  
Bun Chan ◽  
Ying Luo ◽  
Masanari Kimura
Keyword(s):  
Main Group ◽  
Density Functionals

scholarly journals Interactions between large molecules pose a puzzle for reference quantum mechanical methods

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yasmine S. Al-Hamdani ◽  
Péter R. Nagy ◽  
Andrea Zen ◽  
Dennis Barton ◽  
Mihály Kállay ◽  
...  
Keyword(s):  
Experimental Information ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Small Organic Molecules ◽  
Large Molecules ◽  
Reference Information ◽  
Mechanical Methods ◽  
Non Covalent Interactions ◽  
Semi Empirical ◽  
Covalent Interactions

AbstractQuantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol−1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

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