A comparison of the B3LYP and MP2 methods in the calculation of phosphate complexes

Murashov, Vladimir; Leszczyński, Jerzy

doi:10.1016/s0166-1280(00)00524-8

Cited by 30 publications

(23 citation statements)

References 48 publications

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“…Additional non-hydrated Sarin optimizations were also performed using the MP2 method. It has been demonstrated that heavy-atom diffuse and polarization functions are necessary to correctly describe phosphate hydrogen bonding [15]. Sarin is optically active with a chiral phosphate group, but only the S p isomer was evaluated for these calculations.…”

Section: Computational Detailsmentioning

confidence: 99%

“…Details of the H 2 O-phosphate hydrogen bond formation can be probed by calculating and comparing induced IR shifts for a wide range of hydrated clusters. Previous ab initio studies have predicted a reduction (red shift) in the P=O vibrational frequency of 30 cm −1 for the monohydrated DMP anion, a red shift of 32 cm −1 for the trihydrated DMP cluster [14,15], while the mono-hydrated DMMP cluster experienced a 21 cm −1 red shift [23]. The impact on other IR vibrations has also been discussed, including Lee and co-worker's simulation of the water complexation with DMMP, DIFP, Sarin, and Soman (GD).…”

Section: Introductionmentioning

confidence: 96%

“…Ab initio computational methods have previously proven to be useful in investigating OP micro-hydration and include studies of the dihydrogen phosphate (DHP) and dimethyl phosphate (DMP) anion [14][15][16], bisphosphonates [17][18][19], phosphate [20], polyphosphate anions [21], DMMP [22,23], the G-agent simulant diisopropyl fluorophosphate (DIFP), and Sarin [22]. Recently we reported ab initio studies of adsorption energetics for the micro-hydrated Sarin•nH 2 O (n=1-4) clusters, confirming that the primary interaction was hydrogen bonding between the Sarin P=O group and water [24].…”

Section: Introductionmentioning

confidence: 99%

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Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Alam

Pearce

2015

J Mol Model

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The infrared (IR) spectra of micro-hydrated Sarin•(H2O)n clusters containing between one and four explicit waters have been studied using ab initio density functional theory (DFT) methods. The phosphate group P=O bond vibration region (∼1270 to 1290 cm(-1)) revealed the largest frequency variation with hydration, with a frequency red shift reflecting the direct hydrogen bond formation between the P=O of Sarin and water. Small variations to the P-F stretch (∼810 to 815 cm(-1)) and the C-O-P vibrational modes (∼995 to 1004 cm(-1)) showed that the water interactions with these functional groups were minor, and that the structures of Sarin were not extensively perturbed in the hydrated complexes. Increasing the number of explicit hydration waters produced only small vibrational changes in the lowest free energy complexes. These minor changes were consistent with a single water-phosphate hydrogen bond being the dominant structure, though a second water-phosphate hydrogen bond was observed in some complexes and was identified by an additional red shift of the P=O bond vibration. The H2O•H2O vibrational modes (∼3450 to 3660 cm(-1)) increased in complexity with higher hydration levels and reflect the extended hydrogen bonding networks formed between the explicit waters in the hydrated Sarin clusters. Graphical Abstract Ab initio studies of the infrared signature for micro-hydrated Sarin.

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Section: Computational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

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Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Alam

Pearce

2015

J Mol Model

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“…The advantage of studies performed in silico is that all theoretically possible binding modes can be examined and unreasonable interactions ruled out. Recent studies of systems containing bare DMP Ϫ , as well as their complexes with water and some alkali and alkaline earth metals, have [17,18] provided information about the binding affinities of various metal cations and their effect on vibration spectra, although they neglect the cation hydration shells that strongly affect their binding properties. Because calculations of spectroscopic properties performed in gas phase differ significantly from experimental data obtained in condensed media, corrections to the force constants were required [16].…”

mentioning

confidence: 99%

Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium

Petrov

Funseth-Smotzer

Pack

2005

Int J of Quantum Chemistry

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Dimethyl phosphate anion (DMP Ϫ) is often used to simulate the properties of the phosphate group, an important structural fragment of nucleic acids and phospholipids. Besides its functional importance, DMP Ϫ has a strong affinity for metal cations and is often considered to be their binding site. In this study we reevaluate the binding properties of DMP Ϫ with water molecules and with explicitly hydrated magnesium and calcium cations in the presence of a polar continuum solvent. We analyze the stability of the DMP Ϫ in different conformations that represent possible inner-and outer-sphere binding modes. Our previous work (Petrov et al. J Phys Chem B 2004) has shown that electrostatic calculations, particularly those using a point-charge model, are wholly inadequate for this purpose. Calculations were performed at the B3LYP/6-31G(d,p) level of theory within the framework of the COSMO polarized continuum model (CPCM). Our data indicate that magnesium prefers outer-sphere coordination with DMP Ϫ , whereas calcium binds directly. The effect of cation binding on vibrational infrared and Raman spectra are also discussed. We found that the inclusion of polar solvent in the computations improves the agreement between calculated spectral data and experimental results.

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“…Geometries were optimized followed by harmonic vibrational frequency calculations at the same level of theory to confirm all structures were at local minima on the potential energy surface. B3LYP/6-31+G(d) level calculations were performed because it has been cited for its reliability and accuracy of predicting hydrogen bonding interactions at minimal computational cost [19][20][21][22].…”

Section: Theoretical Methods and Computational Detailsmentioning

confidence: 99%

Density functional theory study on the interaction between keto-9H guanine and aspartic acid

Harris

Hill

2011

J Mol Model

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A theoretical study was performed using density functional theory (DFT) to investigate hydrogen bonding interactions in signature complexes formed between keto-9H guanine (Gua) and aspartic acid (Asp) at neutral pH. Optimized geometries, binding energies and the theoretical IR spectra of guanine, aspartic acid and their corresponding complexes (Gua-Asp) were calculated using the B3LYP method and the 6-31+G(d) basis set. Stationary points found to be at local minima on the potential energy surface were verified by second derivative harmonic vibrational frequency calculations at the same level of theory. AIM theory was used to analyze the hydrogen bonding characteristics of these DNA base complex systems. Our results show that the binding motif for the most stable complex is strikingly similar to a Watson-Crick motif observed in the guanine-cytosine base pair. We have found a range of hydrogen bonding interactions between guanine and aspartic acid in the six complexes. This was further verified by theoretical IR spectra of ω(C-H--O-H) cm(-1) stretches for the Gua-Asp complexes. The electron density plot indicates strong hydrogen bonding as shown by the 2p(z) dominant HOMO orbital character.

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A comparison of the B3LYP and MP2 methods in the calculation of phosphate complexes

Cited by 30 publications

References 48 publications

Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Computational study of dimethyl phosphate anion and its complexes with water, magnesium, and calcium

Density functional theory study on the interaction between keto-9H guanine and aspartic acid

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