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1.
Boaz G. Oliveira Regiane C. M. U. Araújo Antônio B. Carvalho Mozart N. Ramos 《Journal of molecular modeling》2009,15(2):123-131
This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C2H4O⋯HF and C2H5N⋯HF) and homocyclic (C3H6⋯HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6–311++G(d,p)
level of theory. Subsequently, the interaction energies and polarizabilities were also evaluated, as well as the infrared
stretch frequencies and absorption intensities. In addition, by combining intermolecular criteria and charge density concepts,
calculations of Bader’s theory of atoms in molecules were used to determine the maxima and minima for electron density in
order to measure the strength of the n⋯H and pπ⋯H hydrogen bonds. Finally, the possibility of an F⋯Hα secondary interaction between the fluoride (F) of hydrogen fluoride and the axial hydrogen atoms (Hα) of the C2H4O and C2H5N heterocyclic rings was explored.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
2.
Density functional theory (DFT) was carried out to identify the existence of intermolecular dihydrogen bonds of the 2-pyridone
(2PY)-diethylmethylsilane (DEMS) and 2PY-triethylgermanium (TEGH) clusters in the ground state. The H···H distances of both
clusters are shorter than the sum of their van der Waals radii. Thus, intermolecular dihydrogen bonds N–H•••H–Si and N–H•••H–Ge
exist in the 2PY-DEMS and 2PY-TEGH clusters, respectively. Based on the ground-state conformations, intermolecular dihydrogen
bonds N–H•••H–Si and N–H•••H–Ge in the electronically excited state of the 2PY-DEMS and 2PY-TEGH clusters were also investigated
using time-dependent density functional theory (TDDFT). Electronic transition of the 2PY-DEMS cluster resembles that of the
2PY-TEGH cluster. Their S1 state is a locally excited (LE) state centered on 2PY moiety. The H•••H distances of the 2PY-DEMS and 2PY-TEGH clusters both
stretch in the S1 state compared to those in the ground state. Upon electronic excitation, intermolecular dihydrogen bonding N–H•••H–Si and
N–H•••H–Ge can weaken with decreasing dihydrogen bonding energies. 相似文献
3.
A statistical analysis of strong and weak hydrogen bonds in the minor groove of DNA was carried out for a set of 70 drug-DNA
complexes. The terms ‘strong’ and ‘weak’ pertain to the inherent strengths and weakness of the donor and acceptor fragments
rather than to any energy considerations. The dataset was extracted from the protein data bank (PDB). The analysis was performed
with an in-house software, hydrogen bond analysis tool (HBAT). In addition to strong hydrogen bonds such as O—H⋯O and N—H⋯O,
the ubiquitous presence of weak hydrogen bonds such as C—H⋯O is implicated in molecular recognition. On an average, there
are 1.4 weak hydrogen bonds for every strong hydrogen bond. For both categories of interaction, the N(3) of purine and the
O(2) of pyrimidine are favoured acceptors. Donor multifurcation is common with the donors generally present in the drug molecules,
and shared by hydrogen bond acceptors in the minor groove. Bifurcation and trifurcation are most commonly observed. The metrics
for strong hydrogen bonds are consistent with established trends. The geometries are variable for weak hydrogen bonds. A database
of recognition geometries for 26 literature amidinium-based inhibitors of Human African Trypanosomes (HAT) was generated with
a docking study using seven inhibitors which occur in published crystal structures included in the list of 70 complexes mentioned
above, and 19 inhibitors for which the drug-DNA complex crystal structures are unknown. The virtual geometries so generated
correlate well with published activities for these 26 inhibitors, justifying our assumption that strong and weak hydrogen
bonds are optimized in the active site. 相似文献
4.
The intermolecular interactions between Aun (n = 3–4) clusters and selected amino acids cysteine and glycine have been investigated by means of density functional theory
(DFT). Present calculations show that the complexes possessing Au-NH2 anchoring bond are found to be energetically favored. The results of NBO and frontier molecular orbitals analysis indicate
that for the complex with anchoring bonds, lone pair electrons of sulfur, oxygen, and nitrogen atoms are transferred to the
antibonding orbitals of gold, while for the complex with the nonconventional hydrogen bonds (Au···H–O), the lone pair electrons
of gold are transferred to the antibonding orbitals of O-H bonds during the interaction. Furthermore, the interaction energy
calculations show that the complexes with Au-NH2 anchoring bond have relatively high intermolecular interaction energy, which is consistent with previous computational studies. 相似文献
5.
Darío J. R. Duarte Margarita M. de las Vallejos Nélida M. Peruchena 《Journal of molecular modeling》2010,16(4):737-748
In this work, the intermolecular distribution of the electronic charge density in the aromatic hydrogen/halogen bonds is studied
within the framework of the atoms in molecules (AIM) theory and the molecular electrostatic potentials (MEP) analysis. The
study is carried out in nine complexes formed between benzene and simple lineal molecules, where hydrogen, fluorine and chlorine
atoms act as bridge atoms. All the results are obtained at MP2 level theory using cc-pVTZ basis set. Attention is focused
on topological features observed at the intermolecular region such as bond, ring and cage critical points of the electron
density, as well as the bond path, the gradient of the density maps, molecular graphs and interatomic surfaces. The strength
of the interaction increases in the following order: F⋅⋅⋅π < Cl⋅⋅⋅π < H⋅⋅⋅π. Our results show that the fluorine atom has the
capability to interact with the π−cloud to form an aromatic halogen bond, as long as the donor group is highly electron withdrawing.
The Laplacian topology allows us to state that the halogen atoms can act as nucleophiles as well as electrophiles, showing
clearly their dual character. 相似文献
6.
Density functional theory was utilized to study the electronic properties of boron nitride (BN) sheets, taking into account
the presence of defects. The structure considered consisted of a central hexagon surrounded by alternating pentagons (three)
and heptagons (three). The isocoronene cluster model with an armchair edge was used with three different chemical compositions.
In the first structure, three B–B bonds were formed where one B in the dimer was part of the central hexagon. In the second
structure, three N–N–N bonds were formed at the periphery of the cluster, around the central hexagon. In the third structure,
three N–N bonds were formed in a similar fashion to the first model. Our results indicated that the third structure was the
most stable configuration; this exhibited planar geometry, semiconductor behavior, and ionic character. To explore the effects
of doping, we replaced B and N atoms with C atoms, considering different atomic positions in the central hexagon. When an
N atom was replaced with a C atom, the new structure was a semiconductor, but when a B atom was replaced with a C atom, the
new structure was a semimetal. At the same time, the polarity increased, inducing covalent behavior. Replacing two N atoms
with two C atoms also resulted in a semiconductor, while replacing two B atoms with two C atoms yielded a semimetal; in both
cases the bonding was covalent. When three B (three N) atoms of the central hexagon were replaced with three C atoms, the
new structure exhibited a transition to a conductor (remained a semiconductor) with low polarity. When monovacancies (N) and
divacancies (B and N) were inserted into the lattice, the system was transformed into a covalent semiconductor. Finally, the
electrostatic potential surface was calculated in order to explore intermolecular properties such as the charge distribution,
which showed how the reactivity of the boron nitride sheets was affected by doping and orbital hybridization. 相似文献
7.
Latosińska JN Latosińska M Tomczak MA Seliger J Zagar V 《Journal of molecular modeling》2011,17(7):1781-1800
The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were
studied experimentally in the solid state via 35Cl NQR, 1H-17O and 1H-14N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O–H···N
hydrogen bonds linking dimers and π–π stacking interactions were described within the QTAIM (quantum theory of atoms in molecules)
/DFT (density functional theory) formalism. Both proton donor and acceptor sites in O–H···N bonds were characterized using
1H-17O and 1H-14N NQDR spectroscopies and QTAIM. The possibility of the existence of O–H···H–O dihydrogen bonds was excluded. The weak intermolecular
interactions in the crystals of clioquinol and cloxiquine were detected and examined. The results obtained in this work suggest
that considerable differences in the NQR parameters for the planar and twisted supramolecular synthons permit differentiation
between specific polymorphic forms, and indicate that the more planar supramolecular synthons are accompanied by a greater
number of weaker hydrogen bonds linking them and stronger π···π stacking interactions. 相似文献
8.
Guedes FL de Oliveira BG Hernandes MZ De Simone CA Veiga FJ de Lima Mdo C Pitta IR Galdino SL Neto PJ 《AAPS PharmSciTech》2011,12(1):401-410
Solid dispersions have been used as a strategy to improve the solubility, dissolution rate, and bioavailability of poor water-soluble
drugs. The increase of the dissolution rate presented by (5Z)-3-(4-chloro-benzyl)-5-(4-nitro-benzylidene)-imidazolidine-2,4-dione (LPSF/FZ4) from the solid dispersions is related to
the existence of intermolecular interactions of hydrogen bond type (>N–H...O<) between the amide group (>N–H) of the LPSF/FZ4 and the ether group (–O–) of the polyethyleneglycol polymer, or the carbonyl
(C=O) of the polyvinylpyrrolidone polymer (PVP). The intensity of these interactions is directly reflected in the morphology
acquired by LPSF/FZ4 in these systems, where a new solid phase, in the form of amorphous aggregates of irregular size, was
identified through scanning electron microscopy and confirmed in the characterizations achieved using X-ray diffraction and
thermal analysis of DSC. The solid dispersions with the polymer PVP, in higher concentrations, were revealed to be the best
option to be used in the formulations of LPSF/FZ4 in both theoretical and experimental studies. 相似文献
9.
Choi JH Niketić SR Djordjević I Clegg W Harrington RW 《Journal of molecular modeling》2012,18(5):2135-2146
The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N′-diacetate; acac = acetylacetonato) has been determined
by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated
by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P21/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) ?, β =101.201(9)° and Z = 4.
The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) ? while the angles
O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N–H⋯O
hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic
properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF),
capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated
on selected chromium(III) complexes with similar ligands. 相似文献
10.
Arvydas Tamulis Vykintas Tamulis 《Origins of life and evolution of the biosphere》2007,37(4-5):473-476
Natural and artificial living cells and their substructures are self-assembling, due to electron correlation interactions
among biological and water molecules, which lead to attractive dispersion forces and hydrogen bonds. Dispersion forces are
weak intermolecular forces that arise from the attractive force between quantum multipoles. A hydrogen bond is a special type
of quantum attractive interaction that exists between an electronegative atom and a hydrogen atom bonded to another electronegative
atom; and this hydrogen atom exist in two quantum states. The best method to simulate these dispersion forces and hydrogen
bonds is to perform quantum mechanical non-local density functional potential calculations of artificial minimal living cells
consisting of around 1,000 atoms. The cell systems studied are based on peptide nucleic acid and are 3.0–4.2 nm in diameter.
The electron tunneling and associated light absorption of the most intense transitions, as calculated by the time dependent
density functional theory method, differs from spectroscopic experiments by only 0.2–0.3 nm, which is within the value of
experiment errors. This agreement implies that the quantum mechanically self-assembled structures of artificial minimal living
cells very closely approximate realistic ones. 相似文献
11.
Joshy P. Yesudas Fareed Bhasha Sayyed Cherumuttathu H. Suresh 《Journal of molecular modeling》2011,17(2):401-413
A hydrogen bond prediction tool HBPredicT is developed for detecting structural water molecules and CH···π interactions in
PDB files of protein-ligand complexes. The program adds the missing hydrogen atoms to the protein, ligands, and oxygen atoms
of water molecules and subsequently all the hydrogen bonds in the complex are located using specific geometrical criteria.
Hydrogen bonds are classified into various types based on (i) donor and acceptor atoms, and interactions such as (ii) protein-protein,
(iii) protein-ligand, (iv) protein-water, (v) ligand-water, (vi) water-water, and (vii) protein-water-ligand. Using the information
in category (vii), the water molecules which form hydrogen bonds with the ligand and the protein simultaneously–the structural
water–is identified and retrieved along with the associated ligand and protein residues. For CH···π interactions, the relevant
portions of the corresponding structures are also extracted in the output. The application potential of this program is tested
using 19 HIV-1 protease and 11 PTP1B inhibitor complexes. All the systems showed presence of structural water molecules and
in several cases, the CH···π interaction between ligand and protein are detected. A rare occurrence of CH···π interactions
emanating from both faces of a phenyl ring of the inhibitor is identified in HIV-1 protease 1D4L. 相似文献
12.
The effect of alkyl substitution (CH3, C2H5, n-C3H7, i-C3H7, and t-C4H9) on the hydrogen bond strengths (H-bond) of substituted amide-alcohol complexes has been systematically explored. B3LYP/aug-cc-pVDZ
method was applied to a total of 215 alkyl substituted amide-alcohol complexes to delineate the effect of substitution on
the H-bond strength; formamide-water complex is taken as reference point. Complexes are classified into five types depending
on the hydrogen donor, acceptor and the site of alkyl substitution (Type-IA, Type-IIA, Type-IB, Type-IIB and Type-III). The
strength of H-bond was correlated with geometrical parameters such as proton-acceptor (H∙∙∙∙Y) distance, the length of proton
donating bond (X–H). In all the complexes N–H and O–H stretching frequencies are red-shifted. The effect of alkyl substitution
on N–H and O–H stretching frequencies were analyzed. Topological parameters like electron density at H∙∙∙∙Y and X–H bond critical
points as derived from atom in molecules (AIM) theory was also evaluated. When C = O group is participating in H-bond, the
strength of H-bond decreases with increasing size of alcohols except for methanol (Type-IA, Type-III and Type-IB complexes).
But it increases with increasing size of alkyl groups on amide and decreases with bulky groups. In the case of N–H group as
H-bond donor, the strength of H-bond increases with increasing size of alcohols (Type-IIA and Type-IIB complexes) whereas
decreases with increasing size of alkyl groups on amide. Type-IA, IIA, IB and IIB complexes exhibit good correlations among
IE, H-bond distance and electron density at bcp. In Type-III complexes, average H-bond distance and sum of electron densities
shows better correlation with IEs than the corresponding individuals. The correlation of IE less with electron density at
RCP compared to sum of electron densities. 相似文献
13.
σ-Hole bonding is a noncovalent interaction between a region of positive electrostatic potential on the outer surface of a
Group V, VI, or VII covalently-bonded atom (a σ-hole) and a region of negative potential on another molecule, e.g., a lone
pair of a Lewis base. We have investigated computationally the occurrence of increased vibration frequencies (blue shifts)
and bond shortening vs decreased frequencies (red shifts) and bond lengthening for the covalent bonds to the atoms having the σ-holes (the σ-hole
donors). Both are possible, depending upon the properties of the donor and the acceptor. Our results are consistent with models
that were developed earlier by Hermansson and by Qian and Krimm in relation to blue vs red shifting in hydrogen bond formation. These models invoke the derivatives of the permanent and the induced dipole moments
of the donor molecule.
Figure Computed electrostatic potential on the molecular surface of Cl-NO2. Color ranges, in kcal mol−1, are: red, greater than 25; yellow, between 10 and 25; green, between 0 and 10; blue, between −4 and 0; purple, more negative
than −4. The chlorine is facing the viewer, to the right. Note the yellow region of positive potential on the outer side of
the chlorine, along the extension of the N–Cl bond. The blue region shows the sides of the chlorine to have negative potentials.
The calculations were at the B3PW91/6–31G(d,p) level. 相似文献
14.
Eight H-bonded complexes between serotonin (5-hydroxy-tryptamine) and water/hydrogen peroxide were studied at the B3LYP and
HF levels of theory, using the 6-31+G(d) basis set. A thermodynamic analysis was performed in order to find the most stable
complex. The calculated bonding parameters showed that the most stable H-bonded complex is formed between serotonin and hydrogen
peroxide by means of the intermolecular H-bond –H2N...H–OOH.
Fig. a Theoretical study of the hydrogen-bonded supersystems serotonin-water/hydrogen peroxide 相似文献
15.
When investigating migration and chemotaxis of leukocytes under agarose polyvinylpyrrolidone (PVP; 11 kg/mol) and polyethyleneglycol
(PEG; 6 kg/mol) were used instead of serum. The highest migration was detected with 0.5–1 mm of PVP. Phagocytosis was not
influenced either by PVP or PEG within a concentration range of 0.01 – 1 mM. 相似文献
16.
Hossein Hooshyar Karim Zare Naser Modirshahla Salah Khanahmadzadeh 《Journal of molecular modeling》2009,15(3):247-256
The effect of the molecular structure on the properties of C = O…HX (X = F, Cl) bonds was investigated in a set of small cyclic
carbonyl compounds, using vibrational spectroscopy and B3LYP/6–311G** calculations. Two main effects were studied: the size
of the ring and the inclusion of oxygen atoms in the ring. In these complexes the C = O and H–X participating bonds in the
hydrogen–bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and band
assignments were reported. Surface potential energy calculations are carried out with scanning HCl and HF near oxygen atom. 相似文献
17.
The contribution of hydrogen bonds to protein-solvent interactions and their impact on structural flexibility and dynamics
of myoglobin are discussed. The shift of vibrational peak frequencies with the temperature of myoglobin in sucrose/water and
glycerol/water solutions is used to probe the expansion of the hydrogen bond network. We observe a characteristic change in
the temperature slope of the O–H stretching frequency at the glass transition which correlates with the discontinuity of the
thermal expansion coefficient. The temperature-difference spectra of the amide bands show the same tendency, indicating that
stronger hydrogen bonding in the bulk affects the main-chain solvent interactions in parallel. However, the hydrogen bond
strength decreases relative to the bulk solvent with increasing cosolvent concentration near the protein surface, which suggests
preferential hydration. Weaker and/or fewer hydrogen bonds are observed at low degrees of hydration. The central O–H stretching
frequency of protein hydration water is red-shifted by 40 cm–1 relative to the bulk. The shift increases towards lower temperatures, consistent with contraction and increasing strength
of the protein-water bonds. The temperature slope shows a discontinuity near 180 K. The contraction of the network has reached
a critical limit which leads to frozen-in structures. This effect may represent the molecular mechanism underlying the dynamic
transition observed for the mean square displacements of the protein atoms and the heme iron of myoglobin.
Received: 10 July 1996 / Accepted: 10 April 1997 相似文献
18.
The hydrogen bonding interactions between noradrenaline (NA) and DMSO were studied with density functional theory (DFT) regarding
their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory
of atoms in molecules (QTAIM) and the natural bond orbital (NBO) analyses were employed to elucidate the hydrogen bonding
interaction characteristics in noradrenaline-DMSO complexes. The H-bonds involving the hydroxyls hydrogen in NA and the O
atom in DMSO are dominant intermolecular H-bonds and are stronger than other H-bonds involving the methyl hydrogen of DMSO
as a H-donor. The weak H-bonds also include a π H-bond which involves the benzene ring as a H-donor or H-acceptor. QTAIM identified
the weak H-bonds formed between the methyl hydrogen of DMSO and the N atom in NA in some complexes (AB5, AB6 and AB7), which cannot be further confirmed by NBO and other methods, so there are probably no interactions between hydrogen and
nitrogen atoms among these complexes. A good linear relationship between logarithmic electron density (lnρ
b
) at the bond critical point (BCP) and structural parameter (δR
H···Y) was found. The formations of new H-bonds in some complexes are helpful to strengthen the original intramolecular H-bond,
this is attributed to the cooperativity of H-bonds in complexes and can be learned from the structure results and the NBO
and QTAIM analyses. Analysis of various physically meaningful contributions arising from the energy decomposition procedures
show that the orbital interactions of H-bond is predominant during the formation of the complex, moreover, both the hydrogen
bonding interaction and the structural deformation are responsible for the stability of the complexes. 相似文献
19.
Complexation of celecoxib with hydroxypropyl β-cyclodextrin (HPβCD) in the presence and absence of 3 hydrophilic polymers—polyvinyl
pyrrolidone (PVP), hydroxypropyl methylcellulose (HPMC), and polyethylene glycol (PEG)—was investigated with an objective
of evaluating the effect of hydrophilic polymers on the complexation and solubilizing efficiencies of HPβCD and on the dissolution
rate of celecoxib from the HPβCD complexes. The phase solubility studies indicated the formation of celecoxib-HPβCD inclusion
complexes at a 1∶1M ratio in solution in both the presence and the absence of hydrophilic polymers. The complexes formed were
quite stable. Addition of hydrophilic polymers markedly enhanced the complexation and solubilizing efficiencies of HPβCD.
Solid inclusion complexes of celecoxib-HPβCD were prepared in 1∶1 and 1∶2 ratios by the kneading method, with and without
the addition of hydrophilic polymers. The solubility and dissolution rate of celecoxib were significantly improved by complexation
with HPβCD. The celecoxib-HPβCD (1∶2) inclusion complex yielded a 36.57-fold increase in the dissolution rate of celecoxib.
The addition of hydrophilic polymers also markedly enhanced the dissolution rate of celecoxib from HPβCD complexes: a 72.60-,
61.25-, and 39.15-fold increase was observed with PVP, HPMC, and PEG, respectively. Differential scanning calorimetry and
X-ray diffractometry indicated stronger drug amorphization and entrapment in HPβCD because of the combined action of HPβCD
and the hydrophilic polymers.
Published: September 29, 2006 相似文献
20.
Proteins tend to undergo irreversible inactivation through several chemical modifications, which is a serious problem in various fields. We have recently found that arginine (Arg) suppresses heat‐induced deamidation and β‐elimination, resulting in the suppression of thermal inactivation of hen egg white lysozyme and bovine pancreas ribonuclease A. Here, we report that poly(ethylene glycol) (PEG) with molecular weight 1,000 acts as a thermoinactivation suppressor for both proteins, especially at higher protein concentrations, while Arg was not effective at higher protein concentrations. This difference suggests that PEG, but not Arg, effectively inhibited intermolecular disulfide exchange among thermally denatured proteins. Investigation of the effects of various polymers including PEG with different molecular weight, poly(vinylpyrolidone) (PVP), and poly(vinyl alchol) on thermoinactivation of proteins, circular dichroism, solution viscosity, and the solubility of reduced and S‐carboxy‐methylated lysozyme indicated that amphiphilic PEG and PVP inhibit intermolecular collision of thermally denatured proteins by preferential interaction with thermally denatured proteins, resulting in the inhibition of intermolecular disulfide exchange. These findings regarding the different mechanisms of the effects of amphiphilic polymers––PEG and PVP––and Arg would expand the capabilities of methods to improve the chemical stability of proteins in solution. Biotechnol. Bioeng. 2012; 109: 2543–2552. © 2012 Wiley Periodicals, Inc. 相似文献