1
|
Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
Collapse
Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
| |
Collapse
|
2
|
Feng W, Li D, Cheng L. Theoretical study on L-H +-L with identical donors: short strong hydrogen bond or not? J Chem Phys 2022; 157:094302. [DOI: 10.1063/5.0103228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Short strong hydrogen bonds (SSHBs) play crucial role in many chemical processes. Recently, as the representative of SSHBs, [F-H-F]- was experimentally observed. [F-H-F]- has a symmetric structure, which can be described as a H+ acid shared by two terminal F- donors (F--H+-F-). To explore whether two identical donors are bound to result in SSHBs, we performed theoretical studies on a series of compounds (L-H+-L) with two identical electron donors (L corresponds to donors containing group 14, 15, 16 and 17 elements). The results show that identical donors do not definitely lead to SSHBs. Instead, typical hydrogen bonds also exist. We found that both electronegativity and basicity contribute to the patterns of hydrogen bonds, where more electronegative and weaker donors benefit to SSHBs. Besides, it was found that zero-point energies also respond to the hydrogen bonding systems. This systemic work is expected to provide more insights into SSHBs.
Collapse
Affiliation(s)
- Wanwan Feng
- Anhui University Department of Chemistry, China
| | - Dan Li
- Anhui University - Qingyuan Campus, China
| | - Longjiu Cheng
- Department of Chemistry, Anhui University College of Chemistry and Chemical Engineering, China
| |
Collapse
|
3
|
Lankau T, Yu CH. A Multi-Center Energy Analysis of the Tunable Proton Affinity of Hydrogen Bonded Cluster Ions. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200900012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
4
|
|
5
|
Shao JX, Gong CM, Li XY, Li J. Unimolecular decomposition mechanism of vinyl alcohol by computational study. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0860-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
6
|
Parveen S, Chandra AK, Zeegers-Huyskens T. Theoretical investigation of the hydrogen bonding interaction between substituted phenols and simple O- and N-bases. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
7
|
Sigalov M, Vainer R, Khodorkovsky V. Strong intramolecular hydrogen bonding within the dimedone–aldehyde adducts. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
8
|
Grabowski SJ, Ugalde JM. High-level ab initio calculations on low barrier hydrogen bonds and proton bound homodimers. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.05.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
9
|
Zierkiewicz W, Michalska D, Zeegers-Huyskens T. Theoretical investigation of the conformation, acidity, basicity and hydrogen bonding ability of halogenated ethers. Phys Chem Chem Phys 2010; 12:13681-91. [PMID: 20856955 DOI: 10.1039/c0cp00192a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | | | | |
Collapse
|
10
|
Hammerum S. Alkyl Radicals as Hydrogen Bond Acceptors: Computational Evidence. J Am Chem Soc 2009; 131:8627-35. [DOI: 10.1021/ja901854t] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Steen Hammerum
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| |
Collapse
|
11
|
Jiang N, Ma J. Theoretical study of proton encircling modes in proton sponges with tetraamido/diamino quaternized macrocycles: the role of π-conjugated and aliphatic bridges. Phys Chem Chem Phys 2009; 11:5100-9. [DOI: 10.1039/b821127b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Basu Baul TS, Mizar A, Chandra AK, Song X, Eng G, Jirásko R, Holcapek M, de Vos D, Linden A. Synthesis, crystal structures, cytotoxicity and qualitative structure-activity relationship (QSAR) of cis-bis{5-[(E)-2-(aryl)-1-diazenyl]quinolinolato}di-n-butyltin(IV) complexes, (n)Bu2Sn(L)2. J Inorg Biochem 2008; 102:1719-30. [PMID: 18571240 DOI: 10.1016/j.jinorgbio.2008.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 04/20/2008] [Accepted: 05/05/2008] [Indexed: 10/22/2022]
Abstract
A series of cis-bis{5-[(E)-2-(aryl)-1-diazenyl]quinolinolato}di-n-butyltin(IV) complexes has been synthesized and characterized by (1)H-, (13)C-, (119)Sn NMR, ESI-MS (electrospray ionization mass spectrometry), IR and (119m)Sn Mössbauer spectroscopic techniques in combination with elemental analyses. The structures of four di-n-butyltin(IV) complexes, viz., (n)Bu(2)Sn(L(3))(2) (3), (n)Bu(2)Sn(L(4))(2) (4), (n)Bu(2)Sn(L(5))(2) (5) and (n)Bu(2)Sn(L(7))(2).0.5C(6)H(6) (7) (LH=5-[(E)-2-(aryl)-1-diazenyl)quinolin-8-ol) were determined by single crystal X-ray diffraction. In general, the complexes were found to adopt a distorted cis-octahedral arrangement around the tin atom. These complexes retain their solid-state structure in non-coordinating solvent as evidenced by (119)Sn and (13)C NMR spectroscopic results. The in vitro cytotoxicity of di-n-butyltin(IV) complexes (3-8) is reported against seven well characterized human tumour cell lines. The basicity of the two quinolinolato donor N and O atoms of the ligands are discussed in relation to the cytotoxicity data.
Collapse
Affiliation(s)
- Tushar S Basu Baul
- Department of Chemistry, North-Eastern Hill University, NEHU Permanent Campus, Umshing, Shillong, Meghalaya 793 022, India.
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Chandra AK, Parveen S, Das S, Zeegers-Huyskens T. Blue shifts of the CH stretching vibrations in hydrogen-bonded and protonated trimethylamine. Effect of hyperconjugation on bond properties. J Comput Chem 2008; 29:1490-6. [DOI: 10.1002/jcc.20910] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
14
|
Zhang RB, Eriksson LA. Effects of OH Radical Addition on Proton Transfer in the Guanine−Cytosine Base Pair. J Phys Chem B 2007; 111:6571-6. [PMID: 17506547 DOI: 10.1021/jp071772l] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Double proton transfer (PT) reactions in guanine-cytosine OH radical adducts are studied by the hybrid density functional B3LYP approach. Concerted and stepwise proton-transfer processes are explored between N1(H) on guanine (G) and N3 on cytosine (C), and between N4(H) on C and O6 on G. All systems except GC6OH display a concerted mechanism. 8OHGC has the highest dissociation energy and is 1.2 kcal/mol more stable than the nonradical GC base pair. The origin of the interactions are investigated through the estimation of intrinsic acid-basic properties of the *OH-X monomer (X = G or C). Solvent effects play a significant role in reducing the dissociation energy. The reactions including *OH-C adducts have significantly lower PT barriers than both the nonradical GC pair and the *OH-G adducts. All reactions are endothermic, with the GC6OH --> GC6OHPT reaction has the lowest reaction energy (4.6 kcal/mol). In accordance with earlier results, the estimated NBO charges show that the G moiety carries a slight negative charge (and C a corresponding positive one) in each adduct. The formation of a partial ion pair may be a potential factor leading to the PT reactions being thermodynamically unfavored.
Collapse
Affiliation(s)
- Ru bo Zhang
- The Institute for Chemical Physics and School of Science, Beijing Institute of Technology, Beijing 100081, China
| | | |
Collapse
|
15
|
Lankau T, Yu CH. The relationship between the bond length and the difference in proton affinities for the observation of heteronuclear low barrier hydrogen bonds. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2006.11.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
16
|
Lankau T, Yu CH. Correlated proton motion in hydrogen bonded systems: tuning proton affinities. Phys Chem Chem Phys 2007; 9:299-310. [PMID: 17186073 DOI: 10.1039/b612945e] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The theorem of matching proton affinities (PA) has been widely used in the analysis of hydrogen bonds. However, most experimental and theoretical investigations have to cope with the problem that the variation of the PA of one partner in the hydrogen bond severely affects the properties of the interface between both molecules. The B3LYP/d95+(d,p) analysis of two hydrogen bonds coupled by a 5-methyl-1H-imidazole molecule showed that it is possible to change the PA of one partner of the hydrogen bond while maintaining the properties of the interface. This technique allowed us to correlate various properties of the hydrogen bond directly with the difference in the PAs between both partners: it is possible to tune the potential energy surface of the bonding hydrogen atom from that of an ordinary hydrogen bond (localized hydrogen atom) to that of a low barrier hydrogen bond (LBHB, delocalized hydrogen atom) just by varying the proton affinity of one partner. This correlation shows clearly that matching PAs are of lesser importance for the formation of a LBHB than the relative energy difference between the two tautomers of the hydrogen bond.
Collapse
Affiliation(s)
- Timm Lankau
- Department of Chemistry, National Tsing Hua University, 101 KuangFu Road Sec. 2, HsinChu, 30013, Taiwan.
| | | |
Collapse
|
17
|
The relationship between the energy of activation for the proton-movement and the difference in proton affinities of bonded partners in double well hydrogen bonds. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.04.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
18
|
Correlation analysis of quantum chemical data and the polarizability effect in H-complexes. Russ Chem Bull 2006. [DOI: 10.1007/s11172-006-0303-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
19
|
Chandra AK, Zeegers-Huyskens T. Theoretical Study of (CH···C)- Hydrogen Bonds in CH4-nXn(X = F, Cl; n = 0, 1, 2) Systems Complexed with Their Homoconjugate and Heteroconjugate Carbanions. J Phys Chem A 2005; 109:12006-13. [PMID: 16366655 DOI: 10.1021/jp054123n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This work deals with a theoretical study of the (CH...C)- hydrogen bonds in CH4, CH3X, and CH2X2 (X = F, Cl) complexed with their homoconjugate and heteroconjugate carbanions. The properties of the complexes are calculated with the B3LYP method using the 6-311++G(d,p) or 6-311++G(2df,2p) basis sets. The deprotonation enthalpies (DPE) of the CH bond or the proton affinities of the carbanions (PA(C-) are calculated as well. All the systems with the exception of the CH4...CHCl2(-) one are characterized by a double minimum potential. In some of the complexes, the (CH(b)...C)- hydrogen bond is linear. In other systems, such as CH3F...CH2F- and CH3F...CHF2(-), there is a large departure from linearity, the systems being stabilized by electrostatic interactions between the nonbonded H of the neutral molecule and the F atom of the carbanion. In the transition state, the (CH(b)...C)- bond is linear, and there is a large contraction of the intermolecular C...C distance. The binding energies vary within a large range, from -1.4 to -11.1 kcal mol(-1) for the stable complexes and -8.6 to -44.1 kcal mol(-1) for the metastable complexes. The energy barriers to proton transfer are between 5 and 20 kcal mol(-1) for the heteroconjugate systems and between 3.8 and 8.3 kcal mol(-1) for the homoconjugate systems. The binding energies of the linear complexes depend exponentially on 1.5DPE - PA(C-), showing that the proton donor is more important than the proton acceptor in determining hydrogen bond strength. The NBO analysis indicates an important electronic reorganization in the two partners. The elongations of the CH bond resulting from the interaction with the carbanion depend on the occupation of the sigma*(CH(b)) antibonding orbitals and on the hybridization of the C bonded to H(b). The frequency shifts of the nu(CH)(A1) stretching vibration range between 15 and 1150 cm(-1). They are linearly correlated to the elongation of the CH(b) bond.
Collapse
Affiliation(s)
- Asit K Chandra
- Department of Chemistry, North Eastern Hill University, Shillong, 793022 India
| | | |
Collapse
|
20
|
|
21
|
|
22
|
Theoretical study of (XYO⋯H⋯OXY)+ (X, Y=H, F, Cl) systems. From the asymmetrical to the symmetrical (O⋯H⋯O)+ hydrogen bonds. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.02.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
23
|
Chandra AK, Michalska D, Wysokiñsky R, Zeegers-Huyskens T. Theoretical Study of the Acidity and Basicity of the Cytosine Tautomers and Their 1:1 Complexes with Water. J Phys Chem A 2004. [DOI: 10.1021/jp040206c] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Asit K. Chandra
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India, Institute of Inorganic Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B-3001 Heverlee, Belgium
| | - Danuta Michalska
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India, Institute of Inorganic Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B-3001 Heverlee, Belgium
| | - Rafat Wysokiñsky
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India, Institute of Inorganic Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B-3001 Heverlee, Belgium
| | - Thérèse Zeegers-Huyskens
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India, Institute of Inorganic Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland, and Department of Chemistry, University of Leuven, 200F Celestijnenlaan, B-3001 Heverlee, Belgium
| |
Collapse
|
24
|
Lee PS, Du W, Boger DL, Jorgensen WL. Energetic Preferences for α,β versus β,γ Unsaturation. J Org Chem 2004; 69:5448-53. [PMID: 15287795 DOI: 10.1021/jo049363y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory has been applied at the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level to examine the energetics of alpha,beta- versus beta,gamma-unsaturation for some common organic functional groups. Specifically, the relative stabilities of allyl-X (H2C=CHCH2X) and 1-propenyl-X (H3CCH=CHX) isomers have been computed for X = methyl, vinyl, phenyl, formyl, acetyl, methoxy, methylthio, methylsulfinyl, methylsulfonyl, sulfamoyl, and methoxysulfonyl, and the results are compared to available experimental data. The intrinsic preference of 3 kcal/mol for the 1-propenyl isomer when X = CH3 is exceeded by 2-4 kcal/mol for first-row conjugating groups, but it is not met for the sulfur-containing groups. In particular, alpha,beta-unsaturation is favored by less than 1 kcal/mol for the sulfone and sulfonamide analogues, while it is preferred by 8 kcal/mol for the vinyl-substituted case. Detailed structural results and torsional energy profiles are also reported.
Collapse
Affiliation(s)
- Patrick S Lee
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
| | | | | | | |
Collapse
|